Starting phenix.real_space_refine on Mon Feb 19 09:13:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/02_2024/8dev_27400_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/02_2024/8dev_27400.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/02_2024/8dev_27400_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/02_2024/8dev_27400_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/02_2024/8dev_27400_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/02_2024/8dev_27400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/02_2024/8dev_27400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/02_2024/8dev_27400_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dev_27400/02_2024/8dev_27400_updated.pdb" } resolution = 3.08 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 19 5.49 5 S 135 5.16 5 C 15631 2.51 5 N 3920 2.21 5 O 4540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A ASP 846": "OD1" <-> "OD2" Residue "A GLU 855": "OE1" <-> "OE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 697": "OE1" <-> "OE2" Residue "B GLU 823": "OE1" <-> "OE2" Residue "B TYR 874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 890": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 421": "OE1" <-> "OE2" Residue "C PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 862": "OE1" <-> "OE2" Residue "C GLU 863": "OE1" <-> "OE2" Residue "C TYR 889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24245 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 7761 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 39, 'TRANS': 997} Chain breaks: 1 Chain: "B" Number of atoms: 7813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 7813 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 40, 'TRANS': 1002} Chain: "C" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7806 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 40, 'TRANS': 1001} Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 81 Unusual residues: {'RE6': 1} Classifications: {'peptide': 10, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 8, None: 1} Not linked: pdbres="RE6 D 1 " pdbres="DAB D 2 " Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Planarities with less than four sites: {'DAB:plan-1': 6, 'RE6:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 242 Unusual residues: {'PTY': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 304 Unusual residues: {'PTY': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 238 Unusual residues: {'PTY': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-2': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 12.81, per 1000 atoms: 0.53 Number of scatterers: 24245 At special positions: 0 Unit cell: (130.152, 158.202, 126.786, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 19 15.00 O 4540 8.00 N 3920 7.00 C 15631 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.07 Conformation dependent library (CDL) restraints added in 4.1 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DLE D 7 " Number of C-beta restraints generated: 5706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 22 sheets defined 51.7% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.35 Creating SS restraints... Processing helix chain 'A' and resid 11 through 28 Processing helix chain 'A' and resid 54 through 69 removed outlier: 5.395A pdb=" N SER A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 113 removed outlier: 3.787A pdb=" N GLU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 161 through 166 removed outlier: 3.687A pdb=" N ARG A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 193 No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 297 through 314 removed outlier: 4.508A pdb=" N LYS A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TYR A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 357 Processing helix chain 'A' and resid 364 through 384 Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 391 through 420 removed outlier: 3.921A pdb=" N MET A 396 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 455 removed outlier: 5.443A pdb=" N GLY A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Proline residue: A 453 - end of helix Processing helix chain 'A' and resid 462 through 493 Proline residue: A 488 - end of helix Processing helix chain 'A' and resid 509 through 533 removed outlier: 3.793A pdb=" N LYS A 530 " --> pdb=" O GLY A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 555 Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.847A pdb=" N SER A 597 " --> pdb=" O GLN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 639 through 653 Processing helix chain 'A' and resid 688 through 704 Processing helix chain 'A' and resid 730 through 733 No H-bonds generated for 'chain 'A' and resid 730 through 733' Processing helix chain 'A' and resid 741 through 751 removed outlier: 4.232A pdb=" N LEU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 782 No H-bonds generated for 'chain 'A' and resid 780 through 782' Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 834 through 847 Processing helix chain 'A' and resid 858 through 864 removed outlier: 3.734A pdb=" N GLU A 862 " --> pdb=" O GLN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 889 removed outlier: 3.688A pdb=" N LEU A 876 " --> pdb=" O ALA A 872 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 878 " --> pdb=" O TYR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 923 removed outlier: 3.997A pdb=" N LEU A 900 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 901 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 902 " --> pdb=" O LEU A 899 " (cutoff:3.500A) Proline residue: A 903 - end of helix removed outlier: 3.536A pdb=" N GLU A 920 " --> pdb=" O ASN A 917 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 921 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 957 removed outlier: 3.669A pdb=" N ALA A 947 " --> pdb=" O MET A 943 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 948 " --> pdb=" O GLY A 944 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 997 removed outlier: 5.199A pdb=" N ARG A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Proline residue: A 981 - end of helix Proline residue: A 995 - end of helix Processing helix chain 'A' and resid 1004 through 1040 removed outlier: 3.569A pdb=" N THR A1022 " --> pdb=" O MET A1018 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.636A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 68 removed outlier: 5.026A pdb=" N SER B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 113 removed outlier: 3.958A pdb=" N GLU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.992A pdb=" N ARG B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 194 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 297 through 314 removed outlier: 3.843A pdb=" N ALA B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 357 removed outlier: 3.797A pdb=" N GLU B 332 " --> pdb=" O SER B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 384 Proline residue: B 371 - end of helix Processing helix chain 'B' and resid 390 through 421 removed outlier: 4.279A pdb=" N GLY B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 456 removed outlier: 5.447A pdb=" N GLY B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Proline residue: B 453 - end of helix removed outlier: 4.236A pdb=" N MET B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 494 removed outlier: 3.971A pdb=" N GLN B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Proline residue: B 488 - end of helix Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 555 removed outlier: 3.516A pdb=" N ARG B 555 " --> pdb=" O PHE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 597 removed outlier: 3.716A pdb=" N LYS B 596 " --> pdb=" O THR B 592 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER B 597 " --> pdb=" O GLN B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 632 Processing helix chain 'B' and resid 639 through 651 Processing helix chain 'B' and resid 688 through 703 Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 741 through 750 Processing helix chain 'B' and resid 774 through 776 No H-bonds generated for 'chain 'B' and resid 774 through 776' Processing helix chain 'B' and resid 780 through 782 No H-bonds generated for 'chain 'B' and resid 780 through 782' Processing helix chain 'B' and resid 834 through 847 Processing helix chain 'B' and resid 858 through 864 removed outlier: 3.685A pdb=" N GLU B 862 " --> pdb=" O GLN B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 889 Processing helix chain 'B' and resid 894 through 923 removed outlier: 4.975A pdb=" N VAL B 901 " --> pdb=" O ALA B 897 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N MET B 902 " --> pdb=" O VAL B 898 " (cutoff:3.500A) Proline residue: B 903 - end of helix removed outlier: 3.692A pdb=" N LEU B 923 " --> pdb=" O PHE B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 963 removed outlier: 3.897A pdb=" N GLN B 963 " --> pdb=" O ASP B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 997 removed outlier: 4.914A pdb=" N ARG B 980 " --> pdb=" O ARG B 976 " (cutoff:3.500A) Proline residue: B 981 - end of helix Proline residue: B 995 - end of helix Processing helix chain 'B' and resid 1006 through 1039 removed outlier: 3.970A pdb=" N THR B1013 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE B1027 " --> pdb=" O LEU B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix Processing helix chain 'C' and resid 2 through 7 removed outlier: 4.212A pdb=" N ASP C 7 " --> pdb=" O LYS C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.599A pdb=" N SER C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 69 Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.611A pdb=" N VAL C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 149 through 165 removed outlier: 4.601A pdb=" N VAL C 161 " --> pdb=" O GLN C 157 " (cutoff:3.500A) Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 241 through 246 removed outlier: 4.288A pdb=" N ASN C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 313 removed outlier: 4.681A pdb=" N LYS C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 357 Processing helix chain 'C' and resid 363 through 384 Proline residue: C 371 - end of helix Processing helix chain 'C' and resid 390 through 399 Processing helix chain 'C' and resid 405 through 421 Processing helix chain 'C' and resid 425 through 435 removed outlier: 3.673A pdb=" N LYS C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 455 removed outlier: 3.767A pdb=" N VAL C 450 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Proline residue: C 453 - end of helix Processing helix chain 'C' and resid 460 through 493 removed outlier: 3.869A pdb=" N THR C 471 " --> pdb=" O GLN C 467 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Proline residue: C 488 - end of helix Processing helix chain 'C' and resid 509 through 531 removed outlier: 3.502A pdb=" N LYS C 530 " --> pdb=" O GLY C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 554 Processing helix chain 'C' and resid 581 through 597 removed outlier: 4.185A pdb=" N SER C 597 " --> pdb=" O GLN C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 653 Processing helix chain 'C' and resid 688 through 702 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 741 through 750 Processing helix chain 'C' and resid 781 through 784 No H-bonds generated for 'chain 'C' and resid 781 through 784' Processing helix chain 'C' and resid 834 through 848 Processing helix chain 'C' and resid 859 through 867 removed outlier: 4.544A pdb=" N GLY C 867 " --> pdb=" O GLU C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 889 Processing helix chain 'C' and resid 894 through 923 removed outlier: 3.883A pdb=" N LEU C 900 " --> pdb=" O LEU C 896 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL C 901 " --> pdb=" O ALA C 897 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N MET C 902 " --> pdb=" O VAL C 898 " (cutoff:3.500A) Proline residue: C 903 - end of helix Processing helix chain 'C' and resid 933 through 961 removed outlier: 3.829A pdb=" N ILE C 953 " --> pdb=" O ASN C 949 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 997 removed outlier: 5.254A pdb=" N ARG C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Proline residue: C 981 - end of helix removed outlier: 3.559A pdb=" N PHE C 989 " --> pdb=" O THR C 985 " (cutoff:3.500A) Proline residue: C 995 - end of helix Processing helix chain 'C' and resid 1004 through 1039 removed outlier: 3.786A pdb=" N THR C1013 " --> pdb=" O ALA C1009 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE C1027 " --> pdb=" O LEU C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.422A pdb=" N SER A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A 83 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 264 through 270 removed outlier: 8.702A pdb=" N ARG A 180 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG A 767 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 757 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 770 " --> pdb=" O TYR A 755 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N TYR A 755 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 215 through 217 removed outlier: 4.144A pdb=" N GLY A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 276 through 279 removed outlier: 6.823A pdb=" N ILE A 625 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 604 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE A 623 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR A 606 " --> pdb=" O MET A 621 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET A 621 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N SER A 608 " --> pdb=" O MET A 619 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET A 619 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 821 through 826 removed outlier: 3.606A pdb=" N LEU A 676 " --> pdb=" O GLY A 826 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 721 through 725 Processing sheet with id= G, first strand: chain 'A' and resid 136 through 141 removed outlier: 6.796A pdb=" N VAL A 289 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE A 139 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET A 287 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 42 through 44 removed outlier: 4.525A pdb=" N SER B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP B 83 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 320 through 322 removed outlier: 6.955A pdb=" N VAL B 289 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 139 " --> pdb=" O MET B 287 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N MET B 287 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET B 141 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR B 285 " --> pdb=" O MET B 141 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 264 through 270 removed outlier: 7.920A pdb=" N ARG B 180 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG B 767 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 757 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 770 " --> pdb=" O TYR B 755 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N TYR B 755 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 215 through 217 removed outlier: 4.148A pdb=" N GLY B 215 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 232 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.591A pdb=" N SER B 276 " --> pdb=" O SER B 608 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 625 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE B 604 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE B 623 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR B 606 " --> pdb=" O MET B 621 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N MET B 621 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER B 608 " --> pdb=" O MET B 619 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N MET B 619 " --> pdb=" O SER B 608 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 821 through 826 Processing sheet with id= N, first strand: chain 'B' and resid 721 through 723 Processing sheet with id= O, first strand: chain 'B' and resid 726 through 728 Processing sheet with id= P, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.953A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 320 through 322 removed outlier: 6.802A pdb=" N VAL C 289 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE C 139 " --> pdb=" O MET C 287 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N MET C 287 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET C 141 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR C 285 " --> pdb=" O MET C 141 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 264 through 270 removed outlier: 8.614A pdb=" N ARG C 180 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG C 767 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 757 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 770 " --> pdb=" O TYR C 755 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TYR C 755 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 276 through 279 removed outlier: 3.514A pdb=" N SER C 608 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE C 625 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE C 604 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE C 623 " --> pdb=" O ILE C 604 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR C 606 " --> pdb=" O MET C 621 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET C 621 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER C 608 " --> pdb=" O MET C 619 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N MET C 619 " --> pdb=" O SER C 608 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 821 through 826 removed outlier: 3.547A pdb=" N GLY C 826 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 721 through 728 Processing sheet with id= V, first strand: chain 'C' and resid 248 through 251 removed outlier: 6.558A pdb=" N ILE C 258 " --> pdb=" O LEU C 249 " (cutoff:3.500A) 1296 hydrogen bonds defined for protein. 3756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.10 Time building geometry restraints manager: 10.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3893 1.31 - 1.43: 5929 1.43 - 1.56: 14516 1.56 - 1.68: 38 1.68 - 1.81: 267 Bond restraints: 24643 Sorted by residual: bond pdb=" C DAB D 4 " pdb=" N DAB D 5 " ideal model delta sigma weight residual 1.329 1.457 -0.128 1.40e-02 5.10e+03 8.38e+01 bond pdb=" C DAB D 9 " pdb=" N DAB D 10 " ideal model delta sigma weight residual 1.329 1.456 -0.127 1.40e-02 5.10e+03 8.21e+01 bond pdb=" C LEU D 8 " pdb=" N DAB D 9 " ideal model delta sigma weight residual 1.329 1.456 -0.127 1.40e-02 5.10e+03 8.19e+01 bond pdb=" C DAB D 10 " pdb=" N THR D 11 " ideal model delta sigma weight residual 1.329 1.454 -0.125 1.40e-02 5.10e+03 7.93e+01 bond pdb=" C THR D 3 " pdb=" N DAB D 4 " ideal model delta sigma weight residual 1.329 1.453 -0.124 1.40e-02 5.10e+03 7.88e+01 ... (remaining 24638 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.84: 639 106.84 - 113.63: 14165 113.63 - 120.42: 9167 120.42 - 127.20: 9102 127.20 - 133.99: 178 Bond angle restraints: 33251 Sorted by residual: angle pdb=" O11 PTY A1106 " pdb=" P1 PTY A1106 " pdb=" O14 PTY A1106 " ideal model delta sigma weight residual 92.90 110.48 -17.58 3.00e+00 1.11e-01 3.43e+01 angle pdb=" N VAL A 968 " pdb=" CA VAL A 968 " pdb=" C VAL A 968 " ideal model delta sigma weight residual 113.53 107.83 5.70 9.80e-01 1.04e+00 3.38e+01 angle pdb=" O11 PTY C1103 " pdb=" P1 PTY C1103 " pdb=" O14 PTY C1103 " ideal model delta sigma weight residual 92.90 109.91 -17.01 3.00e+00 1.11e-01 3.21e+01 angle pdb=" O11 PTY C1102 " pdb=" P1 PTY C1102 " pdb=" O14 PTY C1102 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.12e+01 angle pdb=" O11 PTY B1105 " pdb=" P1 PTY B1105 " pdb=" O14 PTY B1105 " ideal model delta sigma weight residual 92.90 109.61 -16.71 3.00e+00 1.11e-01 3.10e+01 ... (remaining 33246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.46: 14398 33.46 - 66.92: 397 66.92 - 100.38: 55 100.38 - 133.84: 14 133.84 - 167.29: 8 Dihedral angle restraints: 14872 sinusoidal: 5967 harmonic: 8905 Sorted by residual: dihedral pdb=" CA PRO C 221 " pdb=" C PRO C 221 " pdb=" N ALA C 222 " pdb=" CA ALA C 222 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" C3 PTY C1101 " pdb=" O11 PTY C1101 " pdb=" P1 PTY C1101 " pdb=" O12 PTY C1101 " ideal model delta sinusoidal sigma weight residual 300.23 132.94 167.29 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C3 PTY C1106 " pdb=" O11 PTY C1106 " pdb=" P1 PTY C1106 " pdb=" O12 PTY C1106 " ideal model delta sinusoidal sigma weight residual -59.77 107.25 -167.02 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 14869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2547 0.032 - 0.064: 923 0.064 - 0.096: 258 0.096 - 0.128: 130 0.128 - 0.160: 4 Chirality restraints: 3862 Sorted by residual: chirality pdb=" C78 RE6 D 1 " pdb=" C77 RE6 D 1 " pdb=" C79 RE6 D 1 " pdb=" C80 RE6 D 1 " both_signs ideal model delta sigma weight residual False 2.74 2.58 0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA DAB D 9 " pdb=" N DAB D 9 " pdb=" C DAB D 9 " pdb=" CB DAB D 9 " both_signs ideal model delta sigma weight residual False 2.48 2.64 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA LEU C 220 " pdb=" N LEU C 220 " pdb=" C LEU C 220 " pdb=" CB LEU C 220 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 3859 not shown) Planarity restraints: 4159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 994 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO C 995 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 995 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 995 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 796 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO B 797 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 797 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 797 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 220 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO C 221 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " -0.026 5.00e-02 4.00e+02 ... (remaining 4156 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 156 2.57 - 3.15: 20304 3.15 - 3.74: 34174 3.74 - 4.32: 48183 4.32 - 4.90: 84514 Nonbonded interactions: 187331 Sorted by model distance: nonbonded pdb=" OE1 GLU B 58 " pdb=" OG SER B 813 " model vdw 1.991 2.440 nonbonded pdb=" O LYS B 627 " pdb=" NH1 ARG B 632 " model vdw 2.043 2.520 nonbonded pdb=" OG SER A 148 " pdb=" OE1 GLU A 151 " model vdw 2.055 2.440 nonbonded pdb=" OH TYR A 542 " pdb=" O LEU A 900 " model vdw 2.055 2.440 nonbonded pdb=" OH TYR B 465 " pdb=" OE1 GLN B 936 " model vdw 2.056 2.440 ... (remaining 187326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 1042 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C5 or name C6 or name C8 or name N1 or name O10 \ or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O \ 7 or name P1 )) or (resid 1102 and (name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C2 or name C20 or name C5 or name C6 or name C8 or name N1 or name O10 or name O \ 11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or resid 1103 or (resid 1104 and (name C1 or name C11 or name C12 or name \ C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 1105 and (name \ C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or na \ me C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C5 or name C6 o \ r name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 \ or name O30 or name O4 or name O7 or name P1 )) or (resid 1107 and (name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C8 or name O10 or name \ O7 )))) selection = (chain 'B' and (resid 1 through 498 or resid 508 through 1042 or (resid 1102 and \ (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C2 or name C5 or name C6 or name C \ 8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name \ O30 or name O4 or name O7 or name P1 )) or (resid 1103 and (name C1 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C2 or name C20 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or n \ ame O4 or name O7 or name P1 )) or (resid 1104 and (name C11 or name C12 or name \ C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C8 )) or (resid 1105 and (name C1 or name C11 or name C12 or name C2 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C5 or name C6 or na \ me C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or \ name O30 or name O4 or name O7 or name P1 )) or (resid 1106 and (name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C20 or name C21 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C5 or name C6 or name C8 \ or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O \ 30 or name O4 or name O7 or name P1 )) or (resid 1108 and (name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C20 or name C21 or name C22 or name C8 or name O10 or name O7 )))) selection = (chain 'C' and (resid 1 through 498 or resid 508 through 1042 or (resid 1102 and \ (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C2 or name C5 or name C6 or name C \ 8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name \ O30 or name O4 or name O7 or name P1 )) or (resid 1103 and (name C1 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C2 or name C20 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or n \ ame O4 or name O7 or name P1 )) or (resid 1104 and (name C11 or name C12 or name \ C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C8 )) or (resid 1105 and (name C1 or name C11 or name C12 or name C20 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C30 or name C31 or name C32 or name C33 or name C5 or name C6 or name C8 \ or name O10 or name O30 or name O4 or name O7 )) or resid 1106 or resid 1108)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 10.550 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 65.410 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 0.128 24643 Z= 0.349 Angle : 0.906 17.576 33251 Z= 0.391 Chirality : 0.039 0.160 3862 Planarity : 0.004 0.100 4159 Dihedral : 16.815 167.294 9166 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.16 % Allowed : 0.24 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.81 (0.16), residues: 3114 helix: 2.15 (0.13), residues: 1655 sheet: -0.37 (0.26), residues: 423 loop : -1.82 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1016 HIS 0.002 0.001 HIS A 688 PHE 0.011 0.001 PHE C1015 TYR 0.015 0.001 TYR B 49 ARG 0.006 0.000 ARG C 767 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 309 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 521 THR cc_start: 0.8620 (t) cc_final: 0.8362 (m) REVERT: B 984 MET cc_start: 0.8874 (mtp) cc_final: 0.8654 (mtp) REVERT: D 8 LEU cc_start: 0.3480 (OUTLIER) cc_final: 0.3153 (mp) outliers start: 4 outliers final: 0 residues processed: 312 average time/residue: 0.3692 time to fit residues: 184.8878 Evaluate side-chains 259 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 159 optimal weight: 0.0570 chunk 126 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 148 optimal weight: 0.4980 chunk 182 optimal weight: 3.9990 chunk 283 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 165 GLN B 729 ASN B 859 GLN C 672 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24643 Z= 0.165 Angle : 0.525 6.073 33251 Z= 0.268 Chirality : 0.041 0.159 3862 Planarity : 0.004 0.067 4159 Dihedral : 15.241 165.651 3941 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.00 % Allowed : 5.68 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 3114 helix: 2.16 (0.13), residues: 1645 sheet: 0.18 (0.27), residues: 392 loop : -1.65 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 892 HIS 0.002 0.001 HIS C 688 PHE 0.012 0.001 PHE C1015 TYR 0.017 0.001 TYR B 49 ARG 0.006 0.000 ARG C 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 267 time to evaluate : 2.758 Fit side-chains revert: symmetry clash REVERT: A 650 MET cc_start: 0.8531 (mtt) cc_final: 0.8321 (mtm) REVERT: A 769 MET cc_start: 0.7846 (mtt) cc_final: 0.7644 (mtt) REVERT: B 778 MET cc_start: 0.7546 (mmp) cc_final: 0.6783 (mmp) REVERT: B 822 MET cc_start: 0.8277 (mtt) cc_final: 0.7642 (mtt) REVERT: B 984 MET cc_start: 0.8817 (mtp) cc_final: 0.8588 (mtp) outliers start: 25 outliers final: 14 residues processed: 281 average time/residue: 0.3532 time to fit residues: 157.9227 Evaluate side-chains 266 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 252 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 78 optimal weight: 0.0170 chunk 283 optimal weight: 3.9990 chunk 306 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 281 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 ASN C 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24643 Z= 0.236 Angle : 0.528 6.741 33251 Z= 0.270 Chirality : 0.042 0.165 3862 Planarity : 0.004 0.062 4159 Dihedral : 14.082 167.347 3939 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.76 % Allowed : 8.08 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.96 (0.16), residues: 3114 helix: 2.01 (0.13), residues: 1645 sheet: 0.35 (0.27), residues: 403 loop : -1.52 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 892 HIS 0.003 0.001 HIS C 688 PHE 0.013 0.001 PHE C1015 TYR 0.018 0.001 TYR B 49 ARG 0.007 0.001 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 271 time to evaluate : 2.935 Fit side-chains revert: symmetry clash REVERT: B 707 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6498 (pp) REVERT: B 862 GLU cc_start: 0.6994 (pm20) cc_final: 0.6652 (pm20) REVERT: B 902 MET cc_start: 0.8015 (mmt) cc_final: 0.7567 (mmt) REVERT: B 984 MET cc_start: 0.8827 (mtp) cc_final: 0.8622 (mtp) REVERT: C 141 MET cc_start: 0.8279 (mmt) cc_final: 0.7984 (mmt) outliers start: 44 outliers final: 30 residues processed: 301 average time/residue: 0.3574 time to fit residues: 171.2446 Evaluate side-chains 287 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 256 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 7.9990 chunk 213 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 301 optimal weight: 0.5980 chunk 148 optimal weight: 0.0670 chunk 269 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 729 ASN C 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24643 Z= 0.211 Angle : 0.509 6.526 33251 Z= 0.262 Chirality : 0.041 0.169 3862 Planarity : 0.004 0.061 4159 Dihedral : 13.321 165.815 3939 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.12 % Allowed : 9.72 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 1.04 (0.16), residues: 3114 helix: 2.04 (0.13), residues: 1645 sheet: 0.48 (0.27), residues: 400 loop : -1.43 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1016 HIS 0.002 0.001 HIS A 688 PHE 0.014 0.001 PHE C1015 TYR 0.015 0.001 TYR B 49 ARG 0.005 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 264 time to evaluate : 2.722 Fit side-chains revert: symmetry clash REVERT: B 862 GLU cc_start: 0.6940 (pm20) cc_final: 0.6601 (pm20) REVERT: B 902 MET cc_start: 0.8004 (mmt) cc_final: 0.7688 (mmt) REVERT: B 943 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7787 (ttm) outliers start: 53 outliers final: 40 residues processed: 302 average time/residue: 0.3607 time to fit residues: 174.6770 Evaluate side-chains 298 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 257 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 799 SER Chi-restraints excluded: chain C residue 823 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 270 optimal weight: 7.9990 chunk 76 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 729 ASN C 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24643 Z= 0.355 Angle : 0.597 8.228 33251 Z= 0.307 Chirality : 0.045 0.239 3862 Planarity : 0.005 0.067 4159 Dihedral : 13.071 166.466 3939 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.52 % Allowed : 11.08 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.71 (0.15), residues: 3114 helix: 1.71 (0.13), residues: 1650 sheet: 0.20 (0.27), residues: 423 loop : -1.48 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 892 HIS 0.003 0.001 HIS C 522 PHE 0.021 0.002 PHE B 11 TYR 0.020 0.002 TYR A 49 ARG 0.008 0.001 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 264 time to evaluate : 2.789 Fit side-chains REVERT: B 707 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6623 (pp) REVERT: B 862 GLU cc_start: 0.6967 (pm20) cc_final: 0.6502 (pm20) REVERT: C 67 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7510 (mtm-85) outliers start: 63 outliers final: 50 residues processed: 312 average time/residue: 0.3557 time to fit residues: 177.4221 Evaluate side-chains 309 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 258 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 799 SER Chi-restraints excluded: chain C residue 823 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 3.9990 chunk 271 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 729 ASN C 413 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24643 Z= 0.201 Angle : 0.507 7.112 33251 Z= 0.262 Chirality : 0.041 0.216 3862 Planarity : 0.004 0.061 4159 Dihedral : 12.426 174.980 3939 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.72 % Allowed : 11.60 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.96 (0.16), residues: 3114 helix: 1.90 (0.13), residues: 1651 sheet: 0.37 (0.27), residues: 418 loop : -1.36 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1016 HIS 0.002 0.001 HIS B 340 PHE 0.013 0.001 PHE B 11 TYR 0.015 0.001 TYR C 49 ARG 0.005 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 267 time to evaluate : 2.832 Fit side-chains revert: symmetry clash REVERT: B 707 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6501 (pp) REVERT: B 862 GLU cc_start: 0.7031 (pm20) cc_final: 0.6677 (pm20) REVERT: C 67 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7646 (mtm-85) outliers start: 68 outliers final: 51 residues processed: 318 average time/residue: 0.3509 time to fit residues: 178.3835 Evaluate side-chains 312 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 260 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 775 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 300 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 138 optimal weight: 0.1980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 729 ASN C 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24643 Z= 0.198 Angle : 0.502 7.099 33251 Z= 0.258 Chirality : 0.041 0.192 3862 Planarity : 0.004 0.060 4159 Dihedral : 11.814 172.714 3939 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.76 % Allowed : 11.96 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 (0.16), residues: 3114 helix: 2.01 (0.13), residues: 1646 sheet: 0.50 (0.27), residues: 419 loop : -1.29 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1016 HIS 0.002 0.001 HIS A 688 PHE 0.013 0.001 PHE C1015 TYR 0.014 0.001 TYR C 49 ARG 0.009 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 264 time to evaluate : 2.713 Fit side-chains revert: symmetry clash REVERT: B 208 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: B 707 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6446 (pp) REVERT: B 862 GLU cc_start: 0.7090 (pm20) cc_final: 0.6616 (pm20) outliers start: 69 outliers final: 55 residues processed: 317 average time/residue: 0.3442 time to fit residues: 174.5259 Evaluate side-chains 315 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 258 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 775 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 729 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24643 Z= 0.163 Angle : 0.480 7.167 33251 Z= 0.246 Chirality : 0.040 0.193 3862 Planarity : 0.004 0.059 4159 Dihedral : 11.184 158.103 3939 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.32 % Allowed : 12.48 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 1.26 (0.16), residues: 3114 helix: 2.12 (0.13), residues: 1643 sheet: 0.63 (0.27), residues: 416 loop : -1.20 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1016 HIS 0.002 0.000 HIS A 522 PHE 0.012 0.001 PHE C1015 TYR 0.015 0.001 TYR A 383 ARG 0.008 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 264 time to evaluate : 2.633 Fit side-chains revert: symmetry clash REVERT: A 482 LEU cc_start: 0.8466 (tp) cc_final: 0.8235 (tp) REVERT: A 539 MET cc_start: 0.7210 (mmm) cc_final: 0.6867 (mmm) REVERT: A 838 MET cc_start: 0.7982 (mtt) cc_final: 0.7584 (mtm) REVERT: B 208 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: B 707 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6360 (pp) REVERT: B 862 GLU cc_start: 0.7088 (pm20) cc_final: 0.6780 (pm20) REVERT: C 783 ILE cc_start: 0.8841 (tp) cc_final: 0.8580 (tp) outliers start: 58 outliers final: 50 residues processed: 308 average time/residue: 0.3421 time to fit residues: 169.1988 Evaluate side-chains 311 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 259 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 784 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.0970 chunk 288 optimal weight: 0.1980 chunk 262 optimal weight: 0.4980 chunk 280 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 220 optimal weight: 0.4980 chunk 85 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 265 optimal weight: 0.6980 chunk 279 optimal weight: 0.7980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 729 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24643 Z= 0.131 Angle : 0.461 7.509 33251 Z= 0.236 Chirality : 0.039 0.182 3862 Planarity : 0.004 0.057 4159 Dihedral : 10.525 151.210 3939 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.12 % Allowed : 12.95 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 1.48 (0.16), residues: 3114 helix: 2.29 (0.13), residues: 1634 sheet: 0.96 (0.28), residues: 398 loop : -1.14 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1016 HIS 0.001 0.000 HIS A 688 PHE 0.028 0.001 PHE B 939 TYR 0.023 0.001 TYR A 362 ARG 0.007 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 272 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.8398 (tp) cc_final: 0.8076 (tp) REVERT: A 539 MET cc_start: 0.7215 (mmm) cc_final: 0.6902 (mmm) REVERT: A 943 MET cc_start: 0.7650 (ttt) cc_final: 0.7247 (ttt) REVERT: B 409 VAL cc_start: 0.8560 (p) cc_final: 0.8296 (m) REVERT: B 707 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6201 (pp) REVERT: B 862 GLU cc_start: 0.7005 (pm20) cc_final: 0.6691 (pm20) REVERT: C 68 ASN cc_start: 0.8490 (t0) cc_final: 0.7795 (t0) REVERT: C 783 ILE cc_start: 0.8784 (tp) cc_final: 0.8520 (tp) outliers start: 53 outliers final: 41 residues processed: 310 average time/residue: 0.3673 time to fit residues: 183.4771 Evaluate side-chains 304 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 262 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 823 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 1.9990 chunk 296 optimal weight: 0.0470 chunk 180 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 205 optimal weight: 0.8980 chunk 310 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24643 Z= 0.142 Angle : 0.466 8.157 33251 Z= 0.237 Chirality : 0.039 0.253 3862 Planarity : 0.004 0.059 4159 Dihedral : 10.170 152.073 3939 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.08 % Allowed : 13.27 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 1.55 (0.16), residues: 3114 helix: 2.32 (0.13), residues: 1637 sheet: 1.00 (0.28), residues: 398 loop : -1.07 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1016 HIS 0.004 0.000 HIS C 46 PHE 0.012 0.001 PHE C1015 TYR 0.016 0.001 TYR A 383 ARG 0.007 0.000 ARG C 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 266 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.8395 (tp) cc_final: 0.8068 (tp) REVERT: A 539 MET cc_start: 0.7265 (mmm) cc_final: 0.6947 (mmm) REVERT: A 943 MET cc_start: 0.7627 (ttt) cc_final: 0.7288 (ttt) REVERT: B 277 THR cc_start: 0.8969 (m) cc_final: 0.8762 (p) REVERT: B 409 VAL cc_start: 0.8556 (p) cc_final: 0.8278 (m) REVERT: B 707 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6311 (pp) REVERT: B 862 GLU cc_start: 0.7009 (pm20) cc_final: 0.6579 (pm20) REVERT: C 68 ASN cc_start: 0.8468 (t0) cc_final: 0.7787 (t0) REVERT: C 596 LYS cc_start: 0.7151 (tppt) cc_final: 0.6608 (ttmm) REVERT: C 783 ILE cc_start: 0.8780 (tp) cc_final: 0.8520 (tp) outliers start: 52 outliers final: 45 residues processed: 305 average time/residue: 0.3384 time to fit residues: 165.0343 Evaluate side-chains 312 residues out of total 2501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 266 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 823 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.7980 chunk 263 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 228 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.103682 restraints weight = 31241.097| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.87 r_work: 0.3088 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24643 Z= 0.169 Angle : 0.480 8.153 33251 Z= 0.245 Chirality : 0.040 0.245 3862 Planarity : 0.004 0.061 4159 Dihedral : 9.960 152.653 3939 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.12 % Allowed : 13.23 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 1.56 (0.16), residues: 3114 helix: 2.32 (0.13), residues: 1638 sheet: 1.01 (0.28), residues: 398 loop : -1.05 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1016 HIS 0.004 0.001 HIS C 46 PHE 0.013 0.001 PHE C1015 TYR 0.014 0.001 TYR A 362 ARG 0.006 0.000 ARG C 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5105.43 seconds wall clock time: 93 minutes 24.02 seconds (5604.02 seconds total)