Starting phenix.real_space_refine on Mon Jul 22 10:14:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr3_17833/07_2024/8pr3_17833.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr3_17833/07_2024/8pr3_17833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr3_17833/07_2024/8pr3_17833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr3_17833/07_2024/8pr3_17833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr3_17833/07_2024/8pr3_17833.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr3_17833/07_2024/8pr3_17833.cif" } resolution = 3.9 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= 0.001 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 11319 2.51 5 N 3146 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "f PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 655": "OD1" <-> "OD2" Residue "f GLU 721": "OE1" <-> "OE2" Residue "f ASP 849": "OD1" <-> "OD2" Residue "h GLU 444": "OE1" <-> "OE2" Residue "j PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 243": "OE1" <-> "OE2" Residue "j ASP 281": "OD1" <-> "OD2" Residue "m GLU 327": "OE1" <-> "OE2" Residue "m ASP 343": "OD1" <-> "OD2" Residue "m TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 464": "OD1" <-> "OD2" Residue "m PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 687": "OD1" <-> "OD2" Residue "m TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 783": "OE1" <-> "OE2" Residue "m PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 849": "OD1" <-> "OD2" Residue "o ASP 503": "OD1" <-> "OD2" Residue "o GLU 542": "OE1" <-> "OE2" Residue "o GLU 565": "OE1" <-> "OE2" Residue "o ASP 601": "OD1" <-> "OD2" Residue "o GLU 605": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17888 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 880 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 1, 'TRANS': 103} Chain: "C" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 886 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "f" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3449 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 12, 'TRANS': 407} Chain breaks: 1 Chain: "h" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 17, 'TRANS': 353} Chain: "j" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2428 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain breaks: 1 Chain: "m" Number of atoms: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4321 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain breaks: 3 Chain: "o" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 17, 'TRANS': 353} Chain: "E" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 10.03, per 1000 atoms: 0.56 Number of scatterers: 17888 At special positions: 0 Unit cell: (119.667, 124.962, 173.676, 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 72 16.00 O 3351 8.00 N 3146 7.00 C 11319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.62 Conformation dependent library (CDL) restraints added in 3.7 seconds 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4240 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 17 sheets defined 51.9% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'B' and resid 26 through 47 Processing helix chain 'B' and resid 55 through 128 removed outlier: 3.626A pdb=" N ASN B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 47 Processing helix chain 'C' and resid 55 through 128 removed outlier: 3.873A pdb=" N ASN C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing helix chain 'f' and resid 561 through 572 Processing helix chain 'f' and resid 577 through 586 Processing helix chain 'f' and resid 588 through 592 removed outlier: 3.578A pdb=" N LEU f 591 " --> pdb=" O PHE f 588 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE f 592 " --> pdb=" O ASN f 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 588 through 592' Processing helix chain 'f' and resid 596 through 604 removed outlier: 4.267A pdb=" N ALA f 600 " --> pdb=" O HIS f 596 " (cutoff:3.500A) Processing helix chain 'f' and resid 604 through 625 removed outlier: 4.060A pdb=" N VAL f 625 " --> pdb=" O ASP f 621 " (cutoff:3.500A) Processing helix chain 'f' and resid 630 through 637 removed outlier: 3.768A pdb=" N LYS f 634 " --> pdb=" O SER f 630 " (cutoff:3.500A) Processing helix chain 'f' and resid 642 through 670 Processing helix chain 'f' and resid 676 through 691 Processing helix chain 'f' and resid 692 through 694 No H-bonds generated for 'chain 'f' and resid 692 through 694' Processing helix chain 'f' and resid 695 through 710 removed outlier: 3.509A pdb=" N PHE f 699 " --> pdb=" O THR f 695 " (cutoff:3.500A) Processing helix chain 'f' and resid 740 through 754 removed outlier: 3.765A pdb=" N ILE f 744 " --> pdb=" O LEU f 740 " (cutoff:3.500A) Processing helix chain 'f' and resid 761 through 773 Processing helix chain 'f' and resid 774 through 798 removed outlier: 3.571A pdb=" N ALA f 778 " --> pdb=" O LEU f 774 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER f 780 " --> pdb=" O PRO f 776 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG f 798 " --> pdb=" O LYS f 794 " (cutoff:3.500A) Processing helix chain 'f' and resid 799 through 804 removed outlier: 3.740A pdb=" N SER f 802 " --> pdb=" O ASN f 799 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU f 803 " --> pdb=" O THR f 800 " (cutoff:3.500A) Processing helix chain 'f' and resid 805 through 820 Processing helix chain 'f' and resid 828 through 863 removed outlier: 3.665A pdb=" N TYR f 832 " --> pdb=" O LYS f 828 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL f 833 " --> pdb=" O LEU f 829 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN f 834 " --> pdb=" O ASP f 830 " (cutoff:3.500A) Processing helix chain 'f' and resid 870 through 891 removed outlier: 3.705A pdb=" N HIS f 891 " --> pdb=" O ASP f 887 " (cutoff:3.500A) Processing helix chain 'f' and resid 895 through 923 removed outlier: 3.661A pdb=" N GLU f 906 " --> pdb=" O LYS f 902 " (cutoff:3.500A) Processing helix chain 'f' and resid 986 through 995 removed outlier: 3.926A pdb=" N LYS f 990 " --> pdb=" O MET f 986 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET f 991 " --> pdb=" O PHE f 987 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL f 992 " --> pdb=" O ALA f 988 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL f 993 " --> pdb=" O TRP f 989 " (cutoff:3.500A) Processing helix chain 'f' and resid 1013 through 1018 Processing helix chain 'f' and resid 1030 through 1039 removed outlier: 3.889A pdb=" N ALA f1039 " --> pdb=" O GLU f1035 " (cutoff:3.500A) Processing helix chain 'h' and resid 574 through 579 Processing helix chain 'h' and resid 583 through 608 removed outlier: 3.917A pdb=" N GLU h 603 " --> pdb=" O ARG h 599 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU h 604 " --> pdb=" O ALA h 600 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU h 605 " --> pdb=" O ASP h 601 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA h 606 " --> pdb=" O ALA h 602 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 76 removed outlier: 3.674A pdb=" N LYS j 73 " --> pdb=" O THR j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 117 removed outlier: 4.691A pdb=" N GLY j 117 " --> pdb=" O TYR j 114 " (cutoff:3.500A) Processing helix chain 'j' and resid 118 through 123 removed outlier: 3.654A pdb=" N ALA j 122 " --> pdb=" O LEU j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 141 through 143 No H-bonds generated for 'chain 'j' and resid 141 through 143' Processing helix chain 'j' and resid 144 through 161 removed outlier: 4.241A pdb=" N SER j 148 " --> pdb=" O THR j 144 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP j 161 " --> pdb=" O ARG j 157 " (cutoff:3.500A) Processing helix chain 'j' and resid 168 through 183 Processing helix chain 'j' and resid 233 through 236 Processing helix chain 'j' and resid 237 through 243 removed outlier: 3.566A pdb=" N GLU j 243 " --> pdb=" O VAL j 239 " (cutoff:3.500A) Processing helix chain 'j' and resid 247 through 266 removed outlier: 3.517A pdb=" N HIS j 257 " --> pdb=" O PHE j 253 " (cutoff:3.500A) Processing helix chain 'j' and resid 279 through 293 Processing helix chain 'j' and resid 320 through 325 removed outlier: 3.798A pdb=" N GLU j 325 " --> pdb=" O ILE j 322 " (cutoff:3.500A) Processing helix chain 'j' and resid 358 through 373 removed outlier: 3.694A pdb=" N GLN j 373 " --> pdb=" O LEU j 369 " (cutoff:3.500A) Processing helix chain 'm' and resid 270 through 287 removed outlier: 3.697A pdb=" N GLU m 274 " --> pdb=" O THR m 270 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU m 282 " --> pdb=" O TRP m 278 " (cutoff:3.500A) Processing helix chain 'm' and resid 323 through 337 Proline residue: m 334 - end of helix Processing helix chain 'm' and resid 340 through 347 removed outlier: 4.005A pdb=" N LEU m 344 " --> pdb=" O PRO m 340 " (cutoff:3.500A) Processing helix chain 'm' and resid 349 through 364 Processing helix chain 'm' and resid 373 through 400 Processing helix chain 'm' and resid 401 through 404 removed outlier: 3.506A pdb=" N VAL m 404 " --> pdb=" O LEU m 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 401 through 404' Processing helix chain 'm' and resid 405 through 439 removed outlier: 3.508A pdb=" N PHE m 409 " --> pdb=" O ALA m 405 " (cutoff:3.500A) Processing helix chain 'm' and resid 456 through 484 removed outlier: 5.392A pdb=" N GLN m 472 " --> pdb=" O LYS m 468 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL m 479 " --> pdb=" O GLN m 475 " (cutoff:3.500A) Processing helix chain 'm' and resid 514 through 532 Processing helix chain 'm' and resid 539 through 569 Processing helix chain 'm' and resid 570 through 575 Processing helix chain 'm' and resid 577 through 588 Processing helix chain 'm' and resid 589 through 593 removed outlier: 3.825A pdb=" N VAL m 593 " --> pdb=" O ALA m 590 " (cutoff:3.500A) Processing helix chain 'm' and resid 594 through 601 removed outlier: 3.575A pdb=" N ILE m 601 " --> pdb=" O ILE m 597 " (cutoff:3.500A) Processing helix chain 'm' and resid 602 through 623 removed outlier: 3.702A pdb=" N THR m 606 " --> pdb=" O ARG m 602 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN m 607 " --> pdb=" O GLU m 603 " (cutoff:3.500A) Processing helix chain 'm' and resid 630 through 638 removed outlier: 4.183A pdb=" N LYS m 634 " --> pdb=" O SER m 630 " (cutoff:3.500A) Processing helix chain 'm' and resid 642 through 670 Processing helix chain 'm' and resid 672 through 676 Processing helix chain 'm' and resid 678 through 693 removed outlier: 3.585A pdb=" N LEU m 682 " --> pdb=" O GLU m 678 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS m 692 " --> pdb=" O SER m 688 " (cutoff:3.500A) Processing helix chain 'm' and resid 695 through 710 removed outlier: 3.504A pdb=" N PHE m 699 " --> pdb=" O THR m 695 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN m 710 " --> pdb=" O VAL m 706 " (cutoff:3.500A) Processing helix chain 'm' and resid 742 through 754 removed outlier: 4.156A pdb=" N LEU m 746 " --> pdb=" O GLU m 742 " (cutoff:3.500A) Processing helix chain 'm' and resid 761 through 798 Proline residue: m 776 - end of helix Processing helix chain 'm' and resid 799 through 802 removed outlier: 3.517A pdb=" N SER m 802 " --> pdb=" O ASN m 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 799 through 802' Processing helix chain 'm' and resid 805 through 821 removed outlier: 3.628A pdb=" N LYS m 809 " --> pdb=" O VAL m 805 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS m 810 " --> pdb=" O ALA m 806 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU m 811 " --> pdb=" O GLY m 807 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA m 821 " --> pdb=" O ALA m 817 " (cutoff:3.500A) Processing helix chain 'm' and resid 828 through 854 removed outlier: 3.571A pdb=" N TYR m 832 " --> pdb=" O LYS m 828 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN m 834 " --> pdb=" O ASP m 830 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR m 839 " --> pdb=" O ARG m 835 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE m 852 " --> pdb=" O ASP m 848 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE m 853 " --> pdb=" O ASP m 849 " (cutoff:3.500A) Processing helix chain 'o' and resid 574 through 579 removed outlier: 3.553A pdb=" N VAL o 579 " --> pdb=" O GLU o 575 " (cutoff:3.500A) Processing helix chain 'o' and resid 583 through 608 removed outlier: 4.500A pdb=" N ALA o 593 " --> pdb=" O GLY o 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 439 Processing helix chain 'F' and resid 430 through 439 removed outlier: 3.565A pdb=" N LYS F 439 " --> pdb=" O SER F 435 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'f' and resid 718 through 723 Processing sheet with id=AA2, first strand: chain 'h' and resid 239 through 245 removed outlier: 5.463A pdb=" N LEU h 241 " --> pdb=" O ASP h 572 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP h 572 " --> pdb=" O LEU h 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 256 through 261 removed outlier: 4.345A pdb=" N CYS h 258 " --> pdb=" O SER h 272 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL h 286 " --> pdb=" O TYR h 273 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY h 285 " --> pdb=" O CYS h 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'h' and resid 309 through 314 Processing sheet with id=AA5, first strand: chain 'h' and resid 358 through 365 removed outlier: 3.915A pdb=" N CYS h 360 " --> pdb=" O ILE h 375 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS h 380 " --> pdb=" O SER h 376 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP h 394 " --> pdb=" O SER h 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'h' and resid 408 through 412 removed outlier: 6.876A pdb=" N GLY h 424 " --> pdb=" O THR h 409 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N MET h 411 " --> pdb=" O VAL h 422 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL h 422 " --> pdb=" O MET h 411 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL h 430 " --> pdb=" O MET h 445 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N MET h 445 " --> pdb=" O VAL h 430 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR h 432 " --> pdb=" O SER h 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 453 through 458 removed outlier: 3.557A pdb=" N PHE h 471 " --> pdb=" O TRP h 483 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR h 492 " --> pdb=" O LEU h 482 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 501 through 506 removed outlier: 4.975A pdb=" N ASP h 503 " --> pdb=" O VAL h 517 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL h 517 " --> pdb=" O ASP h 503 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET h 505 " --> pdb=" O ALA h 515 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA h 515 " --> pdb=" O MET h 505 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP h 518 " --> pdb=" O ARG h 522 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ARG h 522 " --> pdb=" O ASP h 518 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA h 537 " --> pdb=" O LEU h 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'j' and resid 86 through 94 removed outlier: 6.061A pdb=" N ASN j 56 " --> pdb=" O LEU j 132 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE j 134 " --> pdb=" O ASN j 56 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU j 58 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL j 136 " --> pdb=" O LEU j 58 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE j 60 " --> pdb=" O VAL j 136 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP j 138 " --> pdb=" O PHE j 60 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE j 270 " --> pdb=" O VAL j 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'o' and resid 239 through 245 removed outlier: 3.651A pdb=" N SER o 240 " --> pdb=" O ASP o 572 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE o 570 " --> pdb=" O ASN o 242 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLN o 244 " --> pdb=" O ILE o 568 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE o 568 " --> pdb=" O GLN o 244 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'o' and resid 256 through 261 removed outlier: 6.272A pdb=" N SER o 272 " --> pdb=" O SER o 257 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU o 259 " --> pdb=" O VAL o 270 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL o 270 " --> pdb=" O LEU o 259 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP o 261 " --> pdb=" O LEU o 268 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU o 268 " --> pdb=" O TRP o 261 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU o 288 " --> pdb=" O ALA o 271 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL o 286 " --> pdb=" O TYR o 273 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR o 301 " --> pdb=" O VAL o 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'o' and resid 309 through 314 Processing sheet with id=AB4, first strand: chain 'o' and resid 358 through 365 removed outlier: 3.871A pdb=" N CYS o 360 " --> pdb=" O ILE o 375 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS o 380 " --> pdb=" O SER o 376 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'o' and resid 399 through 400 Processing sheet with id=AB6, first strand: chain 'o' and resid 411 through 412 removed outlier: 7.016A pdb=" N VAL o 430 " --> pdb=" O MET o 445 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N MET o 445 " --> pdb=" O VAL o 430 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR o 432 " --> pdb=" O SER o 443 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'o' and resid 453 through 458 removed outlier: 3.591A pdb=" N TYR o 492 " --> pdb=" O LEU o 482 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'o' and resid 501 through 506 removed outlier: 6.865A pdb=" N VAL o 517 " --> pdb=" O TYR o 502 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL o 504 " --> pdb=" O ALA o 515 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA o 515 " --> pdb=" O VAL o 504 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TRP o 506 " --> pdb=" O LEU o 513 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU o 513 " --> pdb=" O TRP o 506 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP o 518 " --> pdb=" O ARG o 522 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG o 522 " --> pdb=" O ASP o 518 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA o 537 " --> pdb=" O LEU o 525 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2877 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: 5.48 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5769 1.34 - 1.46: 4115 1.46 - 1.58: 8247 1.58 - 1.71: 1 1.71 - 1.83: 118 Bond restraints: 18250 Sorted by residual: bond pdb=" C ILE m 601 " pdb=" N ARG m 602 " ideal model delta sigma weight residual 1.332 1.296 0.036 1.40e-02 5.10e+03 6.73e+00 bond pdb=" N SER E 438 " pdb=" CA SER E 438 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.90e+00 bond pdb=" CB GLU B 121 " pdb=" CG GLU B 121 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.70e+00 bond pdb=" CB GLN f 610 " pdb=" CG GLN f 610 " ideal model delta sigma weight residual 1.520 1.583 -0.063 3.00e-02 1.11e+03 4.35e+00 bond pdb=" CB GLN f 605 " pdb=" CG GLN f 605 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.65e+00 ... (remaining 18245 not shown) Histogram of bond angle deviations from ideal: 94.31 - 103.11: 90 103.11 - 111.91: 8575 111.91 - 120.71: 9813 120.71 - 129.51: 6042 129.51 - 138.30: 171 Bond angle restraints: 24691 Sorted by residual: angle pdb=" CB MET f 662 " pdb=" CG MET f 662 " pdb=" SD MET f 662 " ideal model delta sigma weight residual 112.70 131.58 -18.88 3.00e+00 1.11e-01 3.96e+01 angle pdb=" CA LEU m 357 " pdb=" CB LEU m 357 " pdb=" CG LEU m 357 " ideal model delta sigma weight residual 116.30 138.30 -22.00 3.50e+00 8.16e-02 3.95e+01 angle pdb=" CA LEU m 393 " pdb=" CB LEU m 393 " pdb=" CG LEU m 393 " ideal model delta sigma weight residual 116.30 138.02 -21.72 3.50e+00 8.16e-02 3.85e+01 angle pdb=" N LEU E 437 " pdb=" CA LEU E 437 " pdb=" C LEU E 437 " ideal model delta sigma weight residual 111.14 117.74 -6.60 1.08e+00 8.57e-01 3.73e+01 angle pdb=" N ASN F 434 " pdb=" CA ASN F 434 " pdb=" C ASN F 434 " ideal model delta sigma weight residual 111.36 105.38 5.98 1.09e+00 8.42e-01 3.01e+01 ... (remaining 24686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 9299 17.81 - 35.62: 1325 35.62 - 53.42: 312 53.42 - 71.23: 70 71.23 - 89.04: 29 Dihedral angle restraints: 11035 sinusoidal: 4522 harmonic: 6513 Sorted by residual: dihedral pdb=" CA PHE m 339 " pdb=" C PHE m 339 " pdb=" N PRO m 340 " pdb=" CA PRO m 340 " ideal model delta harmonic sigma weight residual -180.00 -155.52 -24.48 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA MET o 445 " pdb=" C MET o 445 " pdb=" N PHE o 446 " pdb=" CA PHE o 446 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLU o 444 " pdb=" C GLU o 444 " pdb=" N MET o 445 " pdb=" CA MET o 445 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 11032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1960 0.052 - 0.103: 601 0.103 - 0.155: 133 0.155 - 0.206: 34 0.206 - 0.258: 7 Chirality restraints: 2735 Sorted by residual: chirality pdb=" CB ILE j 134 " pdb=" CA ILE j 134 " pdb=" CG1 ILE j 134 " pdb=" CG2 ILE j 134 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE m 698 " pdb=" CA ILE m 698 " pdb=" CG1 ILE m 698 " pdb=" CG2 ILE m 698 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL m 381 " pdb=" CA VAL m 381 " pdb=" CG1 VAL m 381 " pdb=" CG2 VAL m 381 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2732 not shown) Planarity restraints: 3192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE m 339 " -0.041 2.00e-02 2.50e+03 8.06e-02 6.49e+01 pdb=" C PHE m 339 " 0.139 2.00e-02 2.50e+03 pdb=" O PHE m 339 " -0.052 2.00e-02 2.50e+03 pdb=" N PRO m 340 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG f1003 " -0.291 9.50e-02 1.11e+02 1.31e-01 1.05e+01 pdb=" NE ARG f1003 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG f1003 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG f1003 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG f1003 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP f 849 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.56e+00 pdb=" CG ASP f 849 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP f 849 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP f 849 " 0.017 2.00e-02 2.50e+03 ... (remaining 3189 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4967 2.80 - 3.33: 16656 3.33 - 3.85: 31462 3.85 - 4.38: 33640 4.38 - 4.90: 57977 Nonbonded interactions: 144702 Sorted by model distance: nonbonded pdb=" OG SER h 475 " pdb=" OD1 ASP h 477 " model vdw 2.278 2.440 nonbonded pdb=" OG1 THR h 454 " pdb=" O TYR h 502 " model vdw 2.307 2.440 nonbonded pdb=" O ILE j 287 " pdb=" OG1 THR j 291 " model vdw 2.309 2.440 nonbonded pdb=" O GLU m 783 " pdb=" OG1 THR m 787 " model vdw 2.310 2.440 nonbonded pdb=" O SER j 127 " pdb=" OG1 THR j 131 " model vdw 2.314 2.440 ... (remaining 144697 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 'B' selection = (chain 'C' and resid 24 through 128) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'h' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.470 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 48.040 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.006 0.065 18250 Z= 0.382 Angle : 1.079 22.004 24691 Z= 0.544 Chirality : 0.054 0.258 2735 Planarity : 0.006 0.131 3192 Dihedral : 17.802 89.039 6795 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.94 % Rotamer: Outliers : 0.67 % Allowed : 26.56 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2193 helix: -0.49 (0.14), residues: 1061 sheet: -0.84 (0.28), residues: 335 loop : -0.95 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP h 552 HIS 0.011 0.001 HIS o 400 PHE 0.033 0.002 PHE m 843 TYR 0.022 0.002 TYR h 301 ARG 0.015 0.001 ARG f1020 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 216 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7823 (ttp80) REVERT: B 122 LEU cc_start: 0.9081 (mt) cc_final: 0.8615 (tp) REVERT: C 98 LYS cc_start: 0.9217 (ttmm) cc_final: 0.8906 (ttmm) REVERT: C 103 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8957 (pp30) REVERT: C 123 GLN cc_start: 0.9051 (tp-100) cc_final: 0.8792 (tp-100) REVERT: j 103 ARG cc_start: 0.8329 (mmp-170) cc_final: 0.7784 (mmm160) REVERT: o 310 MET cc_start: 0.8528 (ptp) cc_final: 0.8293 (ptp) REVERT: o 400 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6458 (t-90) outliers start: 13 outliers final: 8 residues processed: 226 average time/residue: 0.3503 time to fit residues: 114.4081 Evaluate side-chains 197 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 188 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 993 VAL Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain m residue 576 LYS Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 400 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 104 optimal weight: 0.3980 chunk 127 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 916 GLN ** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 708 GLN o 469 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18250 Z= 0.157 Angle : 0.573 11.276 24691 Z= 0.292 Chirality : 0.040 0.148 2735 Planarity : 0.004 0.048 3192 Dihedral : 4.687 46.515 2426 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.87 % Favored : 98.08 % Rotamer: Outliers : 2.42 % Allowed : 24.76 % Favored : 72.83 % 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: 0.29 (0.18), residues: 2193 helix: 1.09 (0.16), residues: 1066 sheet: -0.76 (0.26), residues: 373 loop : -0.45 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP j 143 HIS 0.003 0.001 HIS B 76 PHE 0.011 0.001 PHE h 471 TYR 0.013 0.001 TYR o 502 ARG 0.006 0.000 ARG j 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 201 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 MET cc_start: 0.6647 (mmt) cc_final: 0.4016 (tpt) REVERT: C 123 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8765 (tp-100) REVERT: f 605 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7797 (tm-30) REVERT: f 610 GLN cc_start: 0.8190 (tp40) cc_final: 0.7967 (tp40) REVERT: f 1026 MET cc_start: 0.7698 (mmm) cc_final: 0.6978 (tpp) REVERT: m 413 MET cc_start: 0.9193 (ppp) cc_final: 0.8884 (ppp) REVERT: m 846 LYS cc_start: 0.8847 (mmtm) cc_final: 0.8611 (mmtm) REVERT: o 310 MET cc_start: 0.8603 (ptp) cc_final: 0.8402 (mtm) REVERT: o 400 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6513 (t70) outliers start: 47 outliers final: 28 residues processed: 240 average time/residue: 0.3178 time to fit residues: 114.1594 Evaluate side-chains 203 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 717 ILE Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 895 ASN Chi-restraints excluded: chain h residue 278 ASP Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 396 MET Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 156 LEU Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 576 LYS Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 400 HIS Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 525 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 197 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f1009 HIS ** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 373 GLN ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18250 Z= 0.226 Angle : 0.580 12.613 24691 Z= 0.294 Chirality : 0.041 0.150 2735 Planarity : 0.003 0.042 3192 Dihedral : 4.334 42.175 2419 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 3.19 % Allowed : 25.17 % Favored : 71.64 % 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: 0.83 (0.18), residues: 2193 helix: 1.62 (0.16), residues: 1074 sheet: -0.68 (0.26), residues: 365 loop : -0.24 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP j 143 HIS 0.014 0.001 HIS m 769 PHE 0.018 0.001 PHE B 108 TYR 0.015 0.001 TYR o 502 ARG 0.013 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 187 time to evaluate : 2.245 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: B 25 MET cc_start: 0.6389 (mmt) cc_final: 0.4162 (tpt) REVERT: B 98 LYS cc_start: 0.9240 (tppt) cc_final: 0.9021 (tppt) REVERT: C 123 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8774 (tp-100) REVERT: f 605 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7897 (tm-30) REVERT: f 610 GLN cc_start: 0.8403 (tp40) cc_final: 0.8009 (tp40) REVERT: f 1026 MET cc_start: 0.8150 (mmm) cc_final: 0.7401 (tpp) REVERT: j 185 MET cc_start: 0.7815 (ppp) cc_final: 0.7614 (ppp) REVERT: m 622 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9207 (ttmt) REVERT: m 838 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8694 (pp20) REVERT: o 310 MET cc_start: 0.8687 (ptp) cc_final: 0.8464 (mtm) REVERT: o 503 ASP cc_start: 0.8351 (m-30) cc_final: 0.8058 (m-30) REVERT: o 548 ASN cc_start: 0.8903 (t0) cc_final: 0.8507 (t0) outliers start: 62 outliers final: 42 residues processed: 237 average time/residue: 0.3075 time to fit residues: 109.1521 Evaluate side-chains 218 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 174 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 717 ILE Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 895 ASN Chi-restraints excluded: chain h residue 278 ASP Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 456 ILE Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 245 ASP Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain j residue 349 VAL Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 576 LYS Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 622 LYS Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain m residue 838 GLU Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 344 VAL Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 453 ILE Chi-restraints excluded: chain o residue 567 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 189 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 752 ASN ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18250 Z= 0.212 Angle : 0.568 14.003 24691 Z= 0.284 Chirality : 0.040 0.233 2735 Planarity : 0.003 0.040 3192 Dihedral : 4.166 41.945 2417 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.45 % Rotamer: Outliers : 4.22 % Allowed : 24.45 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.18), residues: 2193 helix: 1.94 (0.16), residues: 1065 sheet: -0.86 (0.25), residues: 397 loop : 0.00 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP j 143 HIS 0.013 0.001 HIS m 769 PHE 0.011 0.001 PHE m 582 TYR 0.013 0.001 TYR o 502 ARG 0.005 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 191 time to evaluate : 2.084 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: C 123 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8767 (tp-100) REVERT: f 605 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7921 (tm-30) REVERT: f 610 GLN cc_start: 0.8424 (tp40) cc_final: 0.7948 (tp40) REVERT: f 624 LYS cc_start: 0.9540 (mmmm) cc_final: 0.8942 (mmmm) REVERT: j 277 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: m 622 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9218 (ttmt) REVERT: m 691 MET cc_start: 0.9290 (tpp) cc_final: 0.9057 (tpp) REVERT: o 244 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: o 310 MET cc_start: 0.8642 (ptp) cc_final: 0.8426 (mtm) REVERT: o 445 MET cc_start: 0.8950 (tpp) cc_final: 0.8668 (tpp) REVERT: o 548 ASN cc_start: 0.8942 (t0) cc_final: 0.8661 (t0) outliers start: 82 outliers final: 54 residues processed: 257 average time/residue: 0.3332 time to fit residues: 126.3565 Evaluate side-chains 230 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 173 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain f residue 608 LEU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 717 ILE Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 895 ASN Chi-restraints excluded: chain h residue 278 ASP Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 525 LEU Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 245 ASP Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain j residue 277 GLU Chi-restraints excluded: chain j residue 349 VAL Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 352 LYS Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 472 GLN Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 576 LYS Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 622 LYS Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 344 VAL Chi-restraints excluded: chain o residue 360 CYS Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 409 THR Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 453 ILE Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 561 VAL Chi-restraints excluded: chain o residue 567 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 221 HIS ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18250 Z= 0.290 Angle : 0.604 12.747 24691 Z= 0.306 Chirality : 0.041 0.156 2735 Planarity : 0.003 0.039 3192 Dihedral : 4.248 40.817 2417 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.13 % Rotamer: Outliers : 4.48 % Allowed : 25.12 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 2193 helix: 2.00 (0.16), residues: 1060 sheet: -1.07 (0.25), residues: 411 loop : 0.08 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 483 HIS 0.009 0.001 HIS m 769 PHE 0.025 0.001 PHE m 582 TYR 0.015 0.001 TYR o 502 ARG 0.008 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 175 time to evaluate : 2.266 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: B 108 PHE cc_start: 0.8080 (t80) cc_final: 0.7878 (t80) REVERT: B 123 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8641 (mt0) REVERT: C 105 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9072 (mm-30) REVERT: C 123 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8777 (tp-100) REVERT: f 605 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8018 (tm-30) REVERT: f 610 GLN cc_start: 0.8401 (tp40) cc_final: 0.7773 (tp40) REVERT: f 624 LYS cc_start: 0.9556 (mmmm) cc_final: 0.8939 (mmmm) REVERT: f 987 PHE cc_start: 0.5654 (OUTLIER) cc_final: 0.3988 (p90) REVERT: m 602 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8256 (mmm-85) REVERT: m 691 MET cc_start: 0.9261 (tpp) cc_final: 0.9061 (tpp) REVERT: o 244 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: o 503 ASP cc_start: 0.8358 (m-30) cc_final: 0.8087 (m-30) REVERT: o 548 ASN cc_start: 0.9075 (t0) cc_final: 0.8639 (t0) outliers start: 87 outliers final: 62 residues processed: 247 average time/residue: 0.3319 time to fit residues: 121.6284 Evaluate side-chains 228 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 164 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain f residue 565 THR Chi-restraints excluded: chain f residue 608 LEU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 717 ILE Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 895 ASN Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 278 ASP Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 456 ILE Chi-restraints excluded: chain h residue 507 SER Chi-restraints excluded: chain h residue 525 LEU Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 156 LEU Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 245 ASP Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 472 GLN Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 516 ASP Chi-restraints excluded: chain m residue 557 ILE Chi-restraints excluded: chain m residue 565 THR Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 344 VAL Chi-restraints excluded: chain o residue 360 CYS Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 430 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 453 ILE Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 561 VAL Chi-restraints excluded: chain o residue 567 GLN Chi-restraints excluded: chain o residue 582 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 221 HIS ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 657 GLN m 752 ASN ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18250 Z= 0.230 Angle : 0.592 14.524 24691 Z= 0.295 Chirality : 0.041 0.176 2735 Planarity : 0.003 0.039 3192 Dihedral : 4.101 25.529 2413 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 4.07 % Allowed : 26.15 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 2193 helix: 2.08 (0.16), residues: 1061 sheet: -1.08 (0.25), residues: 411 loop : 0.15 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 483 HIS 0.008 0.001 HIS m 769 PHE 0.024 0.001 PHE m 843 TYR 0.012 0.001 TYR o 502 ARG 0.010 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 183 time to evaluate : 2.166 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: B 25 MET cc_start: 0.6642 (mpp) cc_final: 0.4462 (tpt) REVERT: C 106 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: C 123 GLN cc_start: 0.8983 (tp-100) cc_final: 0.8776 (tp-100) REVERT: f 605 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8015 (tm-30) REVERT: f 610 GLN cc_start: 0.8414 (tp40) cc_final: 0.7752 (tp40) REVERT: f 624 LYS cc_start: 0.9568 (mmmm) cc_final: 0.8939 (mmmm) REVERT: m 413 MET cc_start: 0.9289 (ppp) cc_final: 0.9013 (ppp) REVERT: m 602 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.8230 (mmm-85) REVERT: m 691 MET cc_start: 0.9278 (tpp) cc_final: 0.9064 (tpp) REVERT: o 244 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: o 445 MET cc_start: 0.8993 (tpp) cc_final: 0.8689 (tpp) REVERT: o 548 ASN cc_start: 0.9039 (t0) cc_final: 0.8715 (t0) REVERT: o 572 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8397 (m-30) outliers start: 79 outliers final: 59 residues processed: 247 average time/residue: 0.3239 time to fit residues: 118.4068 Evaluate side-chains 231 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 169 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain f residue 565 THR Chi-restraints excluded: chain f residue 608 LEU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 717 ILE Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 895 ASN Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 278 ASP Chi-restraints excluded: chain h residue 342 THR Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 456 ILE Chi-restraints excluded: chain h residue 525 LEU Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 245 ASP Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 516 ASP Chi-restraints excluded: chain m residue 557 ILE Chi-restraints excluded: chain m residue 565 THR Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 344 VAL Chi-restraints excluded: chain o residue 360 CYS Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 430 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 453 ILE Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 561 VAL Chi-restraints excluded: chain o residue 572 ASP Chi-restraints excluded: chain o residue 582 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 221 HIS ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 752 ASN ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 242 ASN ** o 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18250 Z= 0.250 Angle : 0.616 13.757 24691 Z= 0.306 Chirality : 0.041 0.198 2735 Planarity : 0.003 0.038 3192 Dihedral : 4.105 24.854 2411 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 4.27 % Allowed : 26.66 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 2193 helix: 2.10 (0.16), residues: 1055 sheet: -1.03 (0.25), residues: 409 loop : 0.13 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 483 HIS 0.007 0.001 HIS m 769 PHE 0.024 0.001 PHE m 843 TYR 0.013 0.001 TYR o 502 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 184 time to evaluate : 2.268 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 REVERT: B 56 MET cc_start: 0.6706 (mmm) cc_final: 0.6440 (mmm) REVERT: B 84 ARG cc_start: 0.8302 (mtt180) cc_final: 0.7990 (ttm110) REVERT: B 123 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8696 (mt0) REVERT: C 123 GLN cc_start: 0.8983 (tp-100) cc_final: 0.8779 (tp-100) REVERT: C 128 HIS cc_start: 0.4287 (OUTLIER) cc_final: 0.4069 (p-80) REVERT: f 581 MET cc_start: 0.9497 (ttm) cc_final: 0.9248 (mtp) REVERT: f 605 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8057 (tm-30) REVERT: f 610 GLN cc_start: 0.8428 (tp40) cc_final: 0.7719 (tp40) REVERT: f 624 LYS cc_start: 0.9556 (mmmm) cc_final: 0.8929 (mmmm) REVERT: j 90 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.8030 (p90) REVERT: m 602 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8216 (mmm-85) REVERT: m 691 MET cc_start: 0.9272 (tpp) cc_final: 0.9051 (tpp) REVERT: o 244 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: o 265 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: o 411 MET cc_start: 0.8713 (ttt) cc_final: 0.8479 (ttp) REVERT: o 548 ASN cc_start: 0.9000 (t0) cc_final: 0.8571 (t0) REVERT: o 572 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8470 (m-30) outliers start: 83 outliers final: 66 residues processed: 252 average time/residue: 0.3433 time to fit residues: 126.9011 Evaluate side-chains 248 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 177 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain f residue 565 THR Chi-restraints excluded: chain f residue 608 LEU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 717 ILE Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 801 ILE Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 895 ASN Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 278 ASP Chi-restraints excluded: chain h residue 342 THR Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 456 ILE Chi-restraints excluded: chain h residue 525 LEU Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 90 TYR Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 245 ASP Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain j residue 338 ASP Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 352 LYS Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 516 ASP Chi-restraints excluded: chain m residue 557 ILE Chi-restraints excluded: chain m residue 565 THR Chi-restraints excluded: chain m residue 576 LYS Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 265 TYR Chi-restraints excluded: chain o residue 269 LEU Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 309 VAL Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 344 VAL Chi-restraints excluded: chain o residue 360 CYS Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 430 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 453 ILE Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 561 VAL Chi-restraints excluded: chain o residue 572 ASP Chi-restraints excluded: chain o residue 582 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 221 HIS ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.004 0.042 18250 Z= 0.252 Angle : 0.626 14.953 24691 Z= 0.309 Chirality : 0.041 0.192 2735 Planarity : 0.003 0.038 3192 Dihedral : 4.101 23.631 2411 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 4.22 % Allowed : 27.02 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.19), residues: 2193 helix: 2.03 (0.16), residues: 1067 sheet: -1.08 (0.25), residues: 409 loop : 0.19 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 483 HIS 0.006 0.001 HIS m 473 PHE 0.025 0.001 PHE m 843 TYR 0.015 0.001 TYR o 502 ARG 0.008 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 187 time to evaluate : 2.219 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 revert: symmetry clash REVERT: B 56 MET cc_start: 0.6707 (mmm) cc_final: 0.6455 (mmm) REVERT: B 84 ARG cc_start: 0.8364 (mtt180) cc_final: 0.8056 (ttm110) REVERT: B 123 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8680 (mt0) REVERT: C 123 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8758 (tp-100) REVERT: C 128 HIS cc_start: 0.4524 (OUTLIER) cc_final: 0.4201 (p-80) REVERT: f 581 MET cc_start: 0.9487 (ttm) cc_final: 0.9258 (mtp) REVERT: f 605 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8061 (tm-30) REVERT: f 610 GLN cc_start: 0.8407 (tp40) cc_final: 0.7662 (tp40) REVERT: f 624 LYS cc_start: 0.9560 (mmmm) cc_final: 0.8927 (mmmm) REVERT: f 987 PHE cc_start: 0.5685 (OUTLIER) cc_final: 0.4040 (p90) REVERT: j 163 MET cc_start: 0.7116 (pmm) cc_final: 0.6791 (pmm) REVERT: m 413 MET cc_start: 0.9305 (ppp) cc_final: 0.9057 (ppp) REVERT: m 602 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8224 (mmm-85) REVERT: m 691 MET cc_start: 0.9286 (tpp) cc_final: 0.9079 (tpp) REVERT: o 244 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: o 265 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6897 (m-80) REVERT: o 572 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8405 (m-30) outliers start: 82 outliers final: 68 residues processed: 255 average time/residue: 0.3517 time to fit residues: 130.7028 Evaluate side-chains 253 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 180 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain f residue 565 THR Chi-restraints excluded: chain f residue 608 LEU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 717 ILE Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 801 ILE Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 857 ILE Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 895 ASN Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 278 ASP Chi-restraints excluded: chain h residue 342 THR Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 456 ILE Chi-restraints excluded: chain h residue 525 LEU Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 245 ASP Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 352 LYS Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 516 ASP Chi-restraints excluded: chain m residue 557 ILE Chi-restraints excluded: chain m residue 565 THR Chi-restraints excluded: chain m residue 568 LEU Chi-restraints excluded: chain m residue 576 LYS Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 265 TYR Chi-restraints excluded: chain o residue 269 LEU Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 309 VAL Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 344 VAL Chi-restraints excluded: chain o residue 360 CYS Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 430 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 453 ILE Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 561 VAL Chi-restraints excluded: chain o residue 572 ASP Chi-restraints excluded: chain o residue 582 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 6.9990 chunk 202 optimal weight: 0.3980 chunk 184 optimal weight: 0.9990 chunk 196 optimal weight: 0.3980 chunk 118 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 626 GLN ** f 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 221 HIS ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18250 Z= 0.169 Angle : 0.618 15.350 24691 Z= 0.301 Chirality : 0.041 0.201 2735 Planarity : 0.003 0.062 3192 Dihedral : 3.960 20.675 2411 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.24 % Allowed : 27.84 % Favored : 68.91 % 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: 1.29 (0.19), residues: 2193 helix: 2.08 (0.16), residues: 1069 sheet: -1.02 (0.25), residues: 409 loop : 0.29 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 483 HIS 0.006 0.001 HIS m 769 PHE 0.025 0.001 PHE m 843 TYR 0.011 0.001 TYR o 502 ARG 0.009 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 194 time to evaluate : 2.333 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 REVERT: B 56 MET cc_start: 0.6654 (mmm) cc_final: 0.6399 (mmm) REVERT: B 108 PHE cc_start: 0.7964 (t80) cc_final: 0.7191 (t80) REVERT: B 123 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8681 (mt0) REVERT: C 123 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8730 (tp-100) REVERT: C 128 HIS cc_start: 0.4523 (OUTLIER) cc_final: 0.4269 (p-80) REVERT: f 605 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8059 (tm-30) REVERT: f 610 GLN cc_start: 0.8458 (tp40) cc_final: 0.7744 (tp40) REVERT: f 624 LYS cc_start: 0.9564 (mmmm) cc_final: 0.8923 (mmmm) REVERT: j 163 MET cc_start: 0.7041 (pmm) cc_final: 0.6721 (pmm) REVERT: m 413 MET cc_start: 0.9292 (ppp) cc_final: 0.9028 (ppp) REVERT: m 602 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8168 (mmm-85) REVERT: m 691 MET cc_start: 0.9291 (tpp) cc_final: 0.9075 (tpp) REVERT: o 244 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: o 572 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8572 (m-30) outliers start: 63 outliers final: 51 residues processed: 245 average time/residue: 0.3403 time to fit residues: 122.4702 Evaluate side-chains 237 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 183 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain f residue 565 THR Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 717 ILE Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 857 ILE Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 278 ASP Chi-restraints excluded: chain h residue 342 THR Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 525 LEU Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 245 ASP Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 516 ASP Chi-restraints excluded: chain m residue 576 LYS Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 269 LEU Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 309 VAL Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 409 THR Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 572 ASP Chi-restraints excluded: chain o residue 582 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 221 HIS ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 752 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18250 Z= 0.192 Angle : 0.629 15.818 24691 Z= 0.308 Chirality : 0.041 0.196 2735 Planarity : 0.003 0.064 3192 Dihedral : 3.976 29.497 2411 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.14 % Allowed : 28.26 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 2193 helix: 2.09 (0.16), residues: 1069 sheet: -1.04 (0.25), residues: 409 loop : 0.31 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP m 755 HIS 0.006 0.001 HIS m 769 PHE 0.045 0.001 PHE C 111 TYR 0.014 0.001 TYR o 502 ARG 0.009 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 186 time to evaluate : 2.256 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 REVERT: B 56 MET cc_start: 0.6413 (mmm) cc_final: 0.6167 (mmm) REVERT: B 85 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8353 (tm-30) REVERT: B 108 PHE cc_start: 0.7775 (t80) cc_final: 0.7346 (t80) REVERT: B 123 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8669 (mt0) REVERT: C 123 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8755 (tp-100) REVERT: C 128 HIS cc_start: 0.4551 (OUTLIER) cc_final: 0.4246 (p-80) REVERT: f 605 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8182 (tm-30) REVERT: f 610 GLN cc_start: 0.8540 (tp40) cc_final: 0.7839 (tp40) REVERT: f 624 LYS cc_start: 0.9562 (mmmm) cc_final: 0.8919 (mmmm) REVERT: j 163 MET cc_start: 0.7081 (pmm) cc_final: 0.6791 (pmm) REVERT: m 413 MET cc_start: 0.9282 (ppp) cc_final: 0.9016 (ppp) REVERT: m 602 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8169 (mmm-85) REVERT: m 691 MET cc_start: 0.9289 (tpp) cc_final: 0.9078 (tpp) REVERT: o 244 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: o 445 MET cc_start: 0.8762 (tpp) cc_final: 0.8555 (tpp) REVERT: o 572 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8592 (m-30) outliers start: 61 outliers final: 51 residues processed: 236 average time/residue: 0.3205 time to fit residues: 111.9902 Evaluate side-chains 237 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 183 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 717 ILE Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 857 ILE Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 278 ASP Chi-restraints excluded: chain h residue 342 THR Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 525 LEU Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 516 ASP Chi-restraints excluded: chain m residue 565 THR Chi-restraints excluded: chain m residue 576 LYS Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 269 LEU Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 309 VAL Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 409 THR Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 572 ASP Chi-restraints excluded: chain o residue 582 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 72 optimal weight: 0.0040 chunk 178 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 221 HIS ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 752 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.081541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059561 restraints weight = 70196.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.061408 restraints weight = 36160.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062557 restraints weight = 23832.686| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18250 Z= 0.171 Angle : 0.628 15.690 24691 Z= 0.304 Chirality : 0.041 0.198 2735 Planarity : 0.003 0.058 3192 Dihedral : 3.910 29.970 2411 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.88 % Allowed : 28.46 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.19), residues: 2193 helix: 2.10 (0.16), residues: 1068 sheet: -1.03 (0.25), residues: 409 loop : 0.35 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP m 755 HIS 0.006 0.001 HIS m 769 PHE 0.041 0.001 PHE B 108 TYR 0.012 0.001 TYR o 502 ARG 0.010 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3477.34 seconds wall clock time: 63 minutes 56.96 seconds (3836.96 seconds total)