Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 02:25:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/08_2023/8t2v_40989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/08_2023/8t2v_40989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/08_2023/8t2v_40989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/08_2023/8t2v_40989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/08_2023/8t2v_40989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/08_2023/8t2v_40989_updated.pdb" } resolution = 3.4 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= 0.015 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: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 101 5.16 5 C 8225 2.51 5 N 2209 2.21 5 O 2591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 642": "OE1" <-> "OE2" Residue "A TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 960": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B ASP 596": "OD1" <-> "OD2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "B TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 672": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 13134 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7247 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 946, 7239 Classifications: {'peptide': 946} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 882} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 946, 7239 Classifications: {'peptide': 946} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 882} Chain breaks: 2 bond proxies already assigned to first conformer: 7403 Chain: "B" Number of atoms: 5502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5502 Classifications: {'peptide': 718} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 682} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Unusual residues: {' CA': 5, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 2, 'NAG': 1} Classifications: {'undetermined': 6, 'water': 6} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.50, per 1000 atoms: 0.72 Number of scatterers: 13134 At special positions: 0 Unit cell: (103.68, 166.32, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 101 16.00 Mg 1 11.99 O 2591 8.00 N 2209 7.00 C 8225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.04 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.11 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.07 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.06 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.05 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.06 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 687 " distance=2.05 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 890 " distance=2.06 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 885 " distance=2.04 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.02 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.06 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.07 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.07 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.12 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.07 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.04 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.06 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.06 Simple disulfide: pdb=" SG CYS B 460 " - pdb=" SG CYS B 471 " distance=2.06 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.05 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.06 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 501 " distance=2.05 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 506 " distance=2.04 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.07 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 544 " distance=2.05 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 542 " distance=2.05 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 558 " distance=2.05 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 583 " distance=2.06 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.05 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 586 " distance=2.02 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 598 " distance=2.08 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 604 " distance=2.05 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 655 " distance=2.08 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 635 " distance=2.06 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 631 " distance=2.06 Simple disulfide: pdb=" SG CYS B 663 " - pdb=" SG CYS B 687 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " BETA1-6 " BMA F 3 " - " BMA F 5 " " BMA H 3 " - " BMA H 4 " NAG-ASN " NAG A1105 " - " ASN A 249 " " NAG A1106 " - " ASN A 680 " " NAG A1107 " - " ASN A 570 " " NAG A1108 " - " ASN A 15 " " NAG B 801 " - " ASN B 654 " " NAG C 1 " - " ASN A 931 " " NAG D 1 " - " ASN B 559 " " NAG E 1 " - " ASN B 320 " " NAG F 1 " - " ASN B 371 " " NAG G 1 " - " ASN B 99 " " NAG H 1 " - " ASN B 452 " Time building additional restraints: 5.65 Conformation dependent library (CDL) restraints added in 3.0 seconds 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 23 sheets defined 12.6% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 188 through 191 No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 260 through 263 No H-bonds generated for 'chain 'A' and resid 260 through 263' Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 911 through 915 Processing helix chain 'A' and resid 966 through 990 Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.823A pdb=" N ASP B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 122 through 130 removed outlier: 4.363A pdb=" N ASP B 126 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 128 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 200 through 206 removed outlier: 3.845A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 233 through 236 No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 260 through 263 Processing helix chain 'B' and resid 282 through 285 removed outlier: 4.532A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 312 through 322 removed outlier: 4.502A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 494 through 497 Processing helix chain 'B' and resid 536 through 538 No H-bonds generated for 'chain 'B' and resid 536 through 538' Processing helix chain 'B' and resid 574 through 577 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 612 through 620 removed outlier: 3.722A pdb=" N CYS B 617 " --> pdb=" O GLU B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 717 Processing sheet with id= A, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.704A pdb=" N VAL A 425 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE A 436 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLY A 423 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY A 438 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 421 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 56 removed outlier: 4.069A pdb=" N SER A 22 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= D, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.838A pdb=" N SER A 96 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 173 through 175 Processing sheet with id= F, first strand: chain 'A' and resid 235 through 242 removed outlier: 5.798A pdb=" N GLY A 256 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER A 238 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 254 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA A 240 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU A 252 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 306 through 310 Processing sheet with id= H, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.734A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 393 through 395 removed outlier: 4.517A pdb=" N LEU A 393 " --> pdb=" O ARG A 400 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 585 through 588 Processing sheet with id= K, first strand: chain 'A' and resid 530 through 536 Processing sheet with id= L, first strand: chain 'A' and resid 612 through 619 removed outlier: 4.104A pdb=" N ARG A 661 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 736 through 741 removed outlier: 5.661A pdb=" N LEU A 649 " --> pdb=" O GLU A 688 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU A 688 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL A 651 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU A 686 " --> pdb=" O VAL A 651 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 748 through 755 removed outlier: 7.141A pdb=" N PHE A 908 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE A 815 " --> pdb=" O PHE A 908 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 758 through 760 removed outlier: 9.311A pdb=" N LEU A 759 " --> pdb=" O TRP A 952 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLN A 954 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 922 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLN A 925 " --> pdb=" O PRO A 804 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 87 through 92 removed outlier: 6.128A pdb=" N ILE B 426 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU B 90 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN B 428 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 92 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR B 430 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 97 through 105 Processing sheet with id= R, first strand: chain 'B' and resid 328 through 332 removed outlier: 6.870A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 155 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS B 192 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 454 through 456 Processing sheet with id= T, first strand: chain 'B' and resid 500 through 502 Processing sheet with id= U, first strand: chain 'B' and resid 541 through 543 Processing sheet with id= V, first strand: chain 'B' and resid 580 through 582 Processing sheet with id= W, first strand: chain 'B' and resid 638 through 640 removed outlier: 3.523A pdb=" N ILE B 678 " --> pdb=" O TYR B 670 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1040 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: 4.76 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2227 1.30 - 1.44: 3331 1.44 - 1.57: 7712 1.57 - 1.71: 1 1.71 - 1.85: 128 Bond restraints: 13399 Sorted by residual: bond pdb=" C GLY A 423 " pdb=" O GLY A 423 " ideal model delta sigma weight residual 1.233 1.186 0.047 7.00e-03 2.04e+04 4.49e+01 bond pdb=" C PRO A 433 " pdb=" O PRO A 433 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.16e-02 7.43e+03 4.03e+01 bond pdb=" C SER A 420 " pdb=" O SER A 420 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.14e-02 7.69e+03 3.81e+01 bond pdb=" CA SER B 211 " pdb=" CB SER B 211 " ideal model delta sigma weight residual 1.534 1.458 0.076 1.34e-02 5.57e+03 3.25e+01 bond pdb=" N GLY A 641 " pdb=" CA GLY A 641 " ideal model delta sigma weight residual 1.442 1.483 -0.041 7.70e-03 1.69e+04 2.85e+01 ... (remaining 13394 not shown) Histogram of bond angle deviations from ideal: 94.52 - 102.65: 98 102.65 - 110.79: 3856 110.79 - 118.92: 8229 118.92 - 127.06: 5891 127.06 - 135.19: 150 Bond angle restraints: 18224 Sorted by residual: angle pdb=" C PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 111.56 102.38 9.18 1.09e+00 8.42e-01 7.09e+01 angle pdb=" CA GLY A 387 " pdb=" C GLY A 387 " pdb=" O GLY A 387 " ideal model delta sigma weight residual 122.22 116.88 5.34 6.50e-01 2.37e+00 6.76e+01 angle pdb=" CA GLY B 555 " pdb=" C GLY B 555 " pdb=" O GLY B 555 " ideal model delta sigma weight residual 122.22 117.90 4.32 6.50e-01 2.37e+00 4.41e+01 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 103.30 108.50 -5.20 8.00e-01 1.56e+00 4.22e+01 angle pdb=" CA GLY B 518 " pdb=" C GLY B 518 " pdb=" O GLY B 518 " ideal model delta sigma weight residual 122.22 118.22 4.00 6.50e-01 2.37e+00 3.80e+01 ... (remaining 18219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 6854 18.08 - 36.16: 838 36.16 - 54.24: 216 54.24 - 72.32: 48 72.32 - 90.40: 18 Dihedral angle restraints: 7974 sinusoidal: 3212 harmonic: 4762 Sorted by residual: dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 38 " pdb=" CB CYS B 38 " ideal model delta sinusoidal sigma weight residual -86.00 -176.18 90.18 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS B 549 " pdb=" SG CYS B 549 " pdb=" SG CYS B 558 " pdb=" CB CYS B 558 " ideal model delta sinusoidal sigma weight residual 93.00 -179.32 -87.68 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS B 601 " pdb=" SG CYS B 601 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -164.75 78.75 1 1.00e+01 1.00e-02 7.73e+01 ... (remaining 7971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1863 0.147 - 0.293: 238 0.293 - 0.440: 3 0.440 - 0.587: 1 0.587 - 0.733: 1 Chirality restraints: 2106 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.23e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.88e+01 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.74e+01 ... (remaining 2103 not shown) Planarity restraints: 2365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.145 2.00e-02 2.50e+03 1.25e-01 1.96e+02 pdb=" C7 NAG C 1 " -0.097 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.178 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 308 " -0.077 2.00e-02 2.50e+03 4.86e-02 4.13e+01 pdb=" CG PHE B 308 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 308 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 308 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE B 308 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 308 " -0.027 2.00e-02 2.50e+03 pdb=" CZ PHE B 308 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1106 " 0.064 2.00e-02 2.50e+03 5.44e-02 3.70e+01 pdb=" C7 NAG A1106 " -0.032 2.00e-02 2.50e+03 pdb=" C8 NAG A1106 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG A1106 " -0.082 2.00e-02 2.50e+03 pdb=" O7 NAG A1106 " -0.003 2.00e-02 2.50e+03 ... (remaining 2362 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 75 2.38 - 3.01: 7286 3.01 - 3.64: 19745 3.64 - 4.27: 28742 4.27 - 4.90: 46990 Nonbonded interactions: 102838 Sorted by model distance: nonbonded pdb=" OE1 GLU B 220 " pdb="CA CA B 805 " model vdw 1.751 2.510 nonbonded pdb=" OE1 GLU A 243 " pdb="CA CA A1102 " model vdw 1.789 2.510 nonbonded pdb=" OE2 GLU A 252 " pdb="CA CA A1102 " model vdw 1.794 2.510 nonbonded pdb=" OE2 GLU A 642 " pdb="CA CA A1109 " model vdw 1.822 2.510 nonbonded pdb="MG MG B 804 " pdb=" O HOH B 902 " model vdw 1.906 2.170 ... (remaining 102833 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 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.780 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 41.190 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.100 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.016 0.080 13399 Z= 1.044 Angle : 1.929 11.241 18224 Z= 1.328 Chirality : 0.095 0.733 2106 Planarity : 0.009 0.152 2354 Dihedral : 17.049 90.402 4812 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.06 % Favored : 89.98 % Rotamer Outliers : 5.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -1.99 (0.20), residues: 1657 helix: -0.68 (0.37), residues: 162 sheet: -0.46 (0.23), residues: 478 loop : -1.94 (0.19), residues: 1017 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 51 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 38 residues processed: 124 average time/residue: 0.2775 time to fit residues: 50.3447 Evaluate side-chains 83 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 45 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 1 residues processed: 38 average time/residue: 0.1415 time to fit residues: 11.2832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 HIS B 438 GLN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.102 13399 Z= 0.257 Angle : 0.740 18.487 18224 Z= 0.358 Chirality : 0.047 0.375 2106 Planarity : 0.005 0.139 2354 Dihedral : 5.804 57.116 1809 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.56 % Favored : 94.02 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -1.22 (0.21), residues: 1657 helix: 0.61 (0.43), residues: 163 sheet: -0.26 (0.22), residues: 546 loop : -1.43 (0.20), residues: 948 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 47 time to evaluate : 1.479 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 63 average time/residue: 0.2211 time to fit residues: 23.2746 Evaluate side-chains 56 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1252 time to fit residues: 4.5401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 120 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.085 13399 Z= 0.471 Angle : 0.798 12.031 18224 Z= 0.394 Chirality : 0.048 0.379 2106 Planarity : 0.006 0.136 2354 Dihedral : 5.859 58.796 1809 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.33 % Favored : 91.30 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -1.32 (0.21), residues: 1657 helix: 0.65 (0.42), residues: 163 sheet: -0.43 (0.22), residues: 555 loop : -1.46 (0.21), residues: 939 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 45 time to evaluate : 1.473 Fit side-chains outliers start: 26 outliers final: 16 residues processed: 66 average time/residue: 0.2155 time to fit residues: 23.9086 Evaluate side-chains 62 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1227 time to fit residues: 5.4451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 30.0000 chunk 78 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 13399 Z= 0.297 Angle : 0.707 17.211 18224 Z= 0.343 Chirality : 0.046 0.365 2106 Planarity : 0.005 0.132 2354 Dihedral : 5.616 56.280 1809 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.07 % Favored : 92.75 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -1.17 (0.21), residues: 1657 helix: 0.79 (0.42), residues: 161 sheet: -0.35 (0.22), residues: 564 loop : -1.34 (0.21), residues: 932 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 1.510 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 52 average time/residue: 0.2140 time to fit residues: 19.0814 Evaluate side-chains 46 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 1.504 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1183 time to fit residues: 2.6929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 0.0040 chunk 136 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 13399 Z= 0.199 Angle : 0.665 14.831 18224 Z= 0.318 Chirality : 0.045 0.355 2106 Planarity : 0.005 0.126 2354 Dihedral : 5.287 57.027 1809 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.88 % Favored : 92.93 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.94 (0.21), residues: 1657 helix: 0.89 (0.42), residues: 162 sheet: -0.07 (0.22), residues: 569 loop : -1.28 (0.21), residues: 926 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 1.544 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 61 average time/residue: 0.2097 time to fit residues: 21.8220 Evaluate side-chains 49 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 1.591 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1259 time to fit residues: 3.7489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 50.0000 chunk 39 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 13399 Z= 0.256 Angle : 0.670 13.894 18224 Z= 0.324 Chirality : 0.045 0.359 2106 Planarity : 0.005 0.124 2354 Dihedral : 5.280 58.001 1809 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.55 % Favored : 92.33 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.88 (0.21), residues: 1657 helix: 1.02 (0.43), residues: 162 sheet: -0.02 (0.22), residues: 566 loop : -1.26 (0.21), residues: 929 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 1.511 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 57 average time/residue: 0.2091 time to fit residues: 20.3961 Evaluate side-chains 51 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 1.469 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1251 time to fit residues: 4.4630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 ASN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 13399 Z= 0.296 Angle : 0.690 12.942 18224 Z= 0.333 Chirality : 0.045 0.358 2106 Planarity : 0.005 0.122 2354 Dihedral : 5.334 59.131 1809 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.91 % Favored : 91.97 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.98 (0.21), residues: 1657 helix: 1.01 (0.43), residues: 162 sheet: -0.13 (0.22), residues: 574 loop : -1.31 (0.21), residues: 921 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 1.471 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 49 average time/residue: 0.2422 time to fit residues: 20.2269 Evaluate side-chains 45 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1424 time to fit residues: 3.6391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 13399 Z= 0.277 Angle : 0.681 13.034 18224 Z= 0.329 Chirality : 0.045 0.355 2106 Planarity : 0.005 0.120 2354 Dihedral : 5.317 59.962 1809 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.67 % Favored : 92.21 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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 (0.21), residues: 1657 helix: 1.12 (0.43), residues: 163 sheet: -0.08 (0.22), residues: 570 loop : -1.30 (0.21), residues: 924 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 1.457 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.2474 time to fit residues: 18.5059 Evaluate side-chains 44 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1883 time to fit residues: 3.4347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 140 optimal weight: 7.9990 chunk 147 optimal weight: 0.5980 chunk 97 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 483 GLN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 13399 Z= 0.180 Angle : 0.660 14.180 18224 Z= 0.314 Chirality : 0.045 0.345 2106 Planarity : 0.005 0.117 2354 Dihedral : 5.042 59.262 1809 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.40 % Favored : 93.42 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.78 (0.21), residues: 1657 helix: 1.03 (0.42), residues: 164 sheet: 0.06 (0.22), residues: 570 loop : -1.20 (0.21), residues: 923 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 1.462 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.2303 time to fit residues: 17.6781 Evaluate side-chains 42 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1164 time to fit residues: 2.2025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 164 optimal weight: 50.0000 chunk 151 optimal weight: 10.0000 chunk 130 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 13399 Z= 0.188 Angle : 0.674 14.426 18224 Z= 0.318 Chirality : 0.045 0.347 2106 Planarity : 0.005 0.112 2354 Dihedral : 4.951 58.835 1809 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.10 % Favored : 93.72 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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 (0.21), residues: 1657 helix: 0.97 (0.42), residues: 169 sheet: 0.13 (0.22), residues: 571 loop : -1.12 (0.21), residues: 917 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 1.533 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.2352 time to fit residues: 17.3182 Evaluate side-chains 40 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 120 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 134 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.074590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.048519 restraints weight = 93908.854| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 5.91 r_work: 0.2833 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 13399 Z= 0.171 Angle : 0.667 14.541 18224 Z= 0.313 Chirality : 0.045 0.344 2106 Planarity : 0.005 0.112 2354 Dihedral : 4.823 58.435 1809 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.46 % Favored : 93.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.63 (0.21), residues: 1657 helix: 0.93 (0.42), residues: 169 sheet: 0.19 (0.22), residues: 571 loop : -1.08 (0.21), residues: 917 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2815.98 seconds wall clock time: 51 minutes 53.63 seconds (3113.63 seconds total)