Starting phenix.real_space_refine on Sat Mar 16 08:54:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7u_29824/03_2024/8g7u_29824_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7u_29824/03_2024/8g7u_29824.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7u_29824/03_2024/8g7u_29824_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7u_29824/03_2024/8g7u_29824_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7u_29824/03_2024/8g7u_29824_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7u_29824/03_2024/8g7u_29824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7u_29824/03_2024/8g7u_29824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7u_29824/03_2024/8g7u_29824_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7u_29824/03_2024/8g7u_29824_updated.pdb" } resolution = 4.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 52 5.49 5 S 80 5.16 5 C 8895 2.51 5 N 2424 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C ARG 502": "NH1" <-> "NH2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C ARG 533": "NH1" <-> "NH2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 621": "OE1" <-> "OE2" Residue "C GLU 627": "OE1" <-> "OE2" Residue "C GLU 749": "OE1" <-> "OE2" Residue "C GLU 804": "OE1" <-> "OE2" Residue "C GLU 840": "OE1" <-> "OE2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D ARG 296": "NH1" <-> "NH2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D GLU 384": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14229 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5234 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1424 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5115 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 27, 'TRANS': 603} Chain breaks: 3 Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1415 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 523 Unusual residues: {'GTP': 1} Classifications: {'RNA': 23, 'undetermined': 1} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna3p': 22, None: 1} Not linked: pdbres="GTP X 1 " pdbres=" G X 2 " Chain: "Y" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 516 Unusual residues: {'UTP': 1} Classifications: {'RNA': 23, 'undetermined': 1} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna3p': 22, None: 1} Not linked: pdbres="UTP Y 1 " pdbres=" C Y 2 " Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4328 SG CYS A 813 90.632 21.520 41.450 1.00 83.84 S ATOM 4741 SG CYS A 864 87.352 22.632 37.635 1.00106.15 S ATOM 10849 SG CYS C 810 103.431 77.672 58.361 1.00 20.23 S ATOM 11288 SG CYS C 864 105.544 81.022 58.252 1.00 52.52 S ATOM 11327 SG CYS C 869 102.103 80.659 56.989 1.00 44.16 S Time building chain proxies: 8.15, per 1000 atoms: 0.57 Number of scatterers: 14229 At special positions: 0 Unit cell: (130.045, 117.46, 127.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 80 16.00 P 52 15.00 O 2776 8.00 N 2424 7.00 C 8895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 402 " distance=2.04 Simple disulfide: pdb=" SG CYS D 347 " - pdb=" SG CYS D 402 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.35 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 869 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 810 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 864 " 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 16 sheets defined 34.9% alpha, 10.2% beta 13 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 5.73 Creating SS restraints... Processing helix chain 'A' and resid 245 through 256 removed outlier: 5.188A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 4.697A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.860A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.542A pdb=" N LYS A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 496 No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 507 through 522 removed outlier: 4.270A pdb=" N VAL A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 557 Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.569A pdb=" N ALA A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 602 removed outlier: 4.155A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 638 through 647 removed outlier: 3.618A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 770 removed outlier: 4.495A pdb=" N THR A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 793 Processing helix chain 'A' and resid 838 through 840 No H-bonds generated for 'chain 'A' and resid 838 through 840' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.910A pdb=" N ALA C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Proline residue: C 253 - end of helix Processing helix chain 'C' and resid 269 through 284 removed outlier: 3.836A pdb=" N LEU C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 314 removed outlier: 3.576A pdb=" N PHE C 314 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 337 No H-bonds generated for 'chain 'C' and resid 334 through 337' Processing helix chain 'C' and resid 348 through 356 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 446 through 451 removed outlier: 4.715A pdb=" N GLN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 490 Processing helix chain 'C' and resid 493 through 495 No H-bonds generated for 'chain 'C' and resid 493 through 495' Processing helix chain 'C' and resid 507 through 520 Processing helix chain 'C' and resid 528 through 555 removed outlier: 3.890A pdb=" N ARG C 533 " --> pdb=" O ASP C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 Processing helix chain 'C' and resid 581 through 601 removed outlier: 3.905A pdb=" N LYS C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 624 removed outlier: 3.717A pdb=" N LEU C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 648 Processing helix chain 'C' and resid 747 through 770 removed outlier: 4.006A pdb=" N THR C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 793 removed outlier: 3.686A pdb=" N SER C 793 " --> pdb=" O PHE C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 822 No H-bonds generated for 'chain 'C' and resid 820 through 822' Processing helix chain 'C' and resid 837 through 840 removed outlier: 3.732A pdb=" N GLU C 840 " --> pdb=" O ALA C 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 837 through 840' Processing helix chain 'C' and resid 889 through 891 No H-bonds generated for 'chain 'C' and resid 889 through 891' Processing sheet with id= A, first strand: chain 'A' and resid 261 through 263 removed outlier: 7.205A pdb=" N GLY A 407 " --> pdb=" O ILE A 262 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 294 through 296 Processing sheet with id= C, first strand: chain 'A' and resid 459 through 462 removed outlier: 4.020A pdb=" N PHE A 459 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE A 631 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N TYR A 715 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE A 633 " --> pdb=" O TYR A 715 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 634 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 893 through 895 removed outlier: 3.942A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 823 through 825 Processing sheet with id= F, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.905A pdb=" N HIS A 876 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS A 861 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLY A 874 " --> pdb=" O LYS A 861 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 280 through 282 Processing sheet with id= H, first strand: chain 'B' and resid 312 through 318 Processing sheet with id= I, first strand: chain 'B' and resid 412 through 416 removed outlier: 3.670A pdb=" N GLY B 328 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 327 " --> pdb=" O VAL B 349 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 293 through 296 removed outlier: 6.474A pdb=" N LEU C 368 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE C 296 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE C 370 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN C 404 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE C 371 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C 406 " --> pdb=" O PHE C 371 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 892 through 896 removed outlier: 3.508A pdb=" N LEU C 809 " --> pdb=" O VAL C 893 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS C 818 " --> pdb=" O LEU C 808 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N CYS C 810 " --> pdb=" O LEU C 816 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU C 816 " --> pdb=" O CYS C 810 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 823 through 825 Processing sheet with id= M, first strand: chain 'C' and resid 842 through 845 removed outlier: 3.550A pdb=" N LYS C 861 " --> pdb=" O ARG C 845 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C 857 " --> pdb=" O LYS C 878 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 878 " --> pdb=" O GLU C 857 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS C 876 " --> pdb=" O ARG C 859 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYS C 861 " --> pdb=" O GLY C 874 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY C 874 " --> pdb=" O LYS C 861 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 280 through 282 Processing sheet with id= O, first strand: chain 'D' and resid 301 through 303 removed outlier: 4.271A pdb=" N TRP D 325 " --> pdb=" O TRP D 351 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS D 348 " --> pdb=" O TRP D 360 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 313 through 318 449 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2223 1.29 - 1.43: 4050 1.43 - 1.56: 8152 1.56 - 1.69: 106 1.69 - 1.82: 108 Bond restraints: 14639 Sorted by residual: bond pdb=" C3' UTP Y 1 " pdb=" C4' UTP Y 1 " ideal model delta sigma weight residual 1.654 1.303 0.351 2.00e-02 2.50e+03 3.07e+02 bond pdb=" C2' UTP Y 1 " pdb=" C3' UTP Y 1 " ideal model delta sigma weight residual 1.301 1.618 -0.317 2.00e-02 2.50e+03 2.50e+02 bond pdb=" C4' UTP Y 1 " pdb=" O4' UTP Y 1 " ideal model delta sigma weight residual 1.320 1.578 -0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C1' UTP Y 1 " pdb=" C2' UTP Y 1 " ideal model delta sigma weight residual 1.585 1.333 0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C1' GTP X 1 " pdb=" C2' GTP X 1 " ideal model delta sigma weight residual 1.524 1.286 0.238 2.00e-02 2.50e+03 1.41e+02 ... (remaining 14634 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.54: 481 105.54 - 113.01: 7954 113.01 - 120.49: 6220 120.49 - 127.97: 5157 127.97 - 135.45: 195 Bond angle restraints: 20007 Sorted by residual: angle pdb=" CA VAL C 332 " pdb=" CB VAL C 332 " pdb=" CG1 VAL C 332 " ideal model delta sigma weight residual 110.40 117.42 -7.02 1.70e+00 3.46e-01 1.70e+01 angle pdb=" C ASP A 527 " pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 121.54 129.33 -7.79 1.91e+00 2.74e-01 1.66e+01 angle pdb=" C GLN B 395 " pdb=" N GLU B 396 " pdb=" CA GLU B 396 " ideal model delta sigma weight residual 122.46 127.73 -5.27 1.41e+00 5.03e-01 1.40e+01 angle pdb=" C GLU D 273 " pdb=" N VAL D 274 " pdb=" CA VAL D 274 " ideal model delta sigma weight residual 120.69 125.85 -5.16 1.46e+00 4.69e-01 1.25e+01 angle pdb=" CA CYS C 268 " pdb=" CB CYS C 268 " pdb=" SG CYS C 268 " ideal model delta sigma weight residual 114.40 122.37 -7.97 2.30e+00 1.89e-01 1.20e+01 ... (remaining 20002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7677 17.94 - 35.88: 937 35.88 - 53.82: 189 53.82 - 71.76: 76 71.76 - 89.71: 31 Dihedral angle restraints: 8910 sinusoidal: 4104 harmonic: 4806 Sorted by residual: dihedral pdb=" CA SER A 855 " pdb=" C SER A 855 " pdb=" N PHE A 856 " pdb=" CA PHE A 856 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA THR C 347 " pdb=" C THR C 347 " pdb=" N PRO C 348 " pdb=" CA PRO C 348 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA PHE A 856 " pdb=" C PHE A 856 " pdb=" N GLU A 857 " pdb=" CA GLU A 857 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1650 0.057 - 0.115: 459 0.115 - 0.172: 114 0.172 - 0.230: 17 0.230 - 0.287: 4 Chirality restraints: 2244 Sorted by residual: chirality pdb=" CB VAL A 522 " pdb=" CA VAL A 522 " pdb=" CG1 VAL A 522 " pdb=" CG2 VAL A 522 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB VAL C 332 " pdb=" CA VAL C 332 " pdb=" CG1 VAL C 332 " pdb=" CG2 VAL C 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE A 345 " pdb=" CA ILE A 345 " pdb=" CG1 ILE A 345 " pdb=" CG2 ILE A 345 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2241 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 261 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ILE A 261 " -0.065 2.00e-02 2.50e+03 pdb=" O ILE A 261 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE A 262 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 381 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO C 382 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 286 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO D 287 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 287 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 287 " -0.036 5.00e-02 4.00e+02 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 193 2.62 - 3.19: 11872 3.19 - 3.76: 23033 3.76 - 4.33: 29475 4.33 - 4.90: 47120 Nonbonded interactions: 111693 Sorted by model distance: nonbonded pdb=" O2' UTP Y 1 " pdb=" OP2 C Y 2 " model vdw 2.056 2.440 nonbonded pdb=" C3' GTP X 1 " pdb=" OP2 G X 2 " model vdw 2.058 2.776 nonbonded pdb=" O2' UTP Y 1 " pdb=" P C Y 2 " model vdw 2.068 3.400 nonbonded pdb=" OG SER C 698 " pdb=" OH TYR C 717 " model vdw 2.234 2.440 nonbonded pdb=" O SER C 855 " pdb=" OG SER C 855 " model vdw 2.288 2.440 ... (remaining 111688 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 241 through 661 or resid 690 through 699 or resid 709 thro \ ugh 718 or resid 734 through 922 or resid 1001)) selection = (chain 'C' and (resid 241 through 922 or resid 1001)) } ncs_group { reference = (chain 'B' and (resid 252 through 343 or (resid 344 and (name N or name CA or na \ me C or name O or name CB )) or resid 345 through 360 or resid 364 through 430)) \ selection = (chain 'D' and (resid 252 through 360 or resid 364 through 430)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.020 Extract box with map and model: 4.640 Check model and map are aligned: 0.240 Set scattering table: 0.120 Process input model: 43.530 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 : 0.009 0.351 14639 Z= 0.553 Angle : 0.947 10.446 20007 Z= 0.513 Chirality : 0.057 0.287 2244 Planarity : 0.007 0.083 2361 Dihedral : 17.292 89.706 5776 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.61 % Allowed : 12.24 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.17), residues: 1610 helix: -1.95 (0.16), residues: 584 sheet: -2.69 (0.29), residues: 288 loop : -3.18 (0.19), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 908 HIS 0.012 0.002 HIS C 847 PHE 0.029 0.003 PHE A 842 TYR 0.019 0.002 TYR D 400 ARG 0.009 0.001 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 216 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 ILE cc_start: 0.7695 (mp) cc_final: 0.7262 (mp) REVERT: A 760 MET cc_start: 0.4703 (ppp) cc_final: 0.3432 (ppp) REVERT: B 324 HIS cc_start: 0.6566 (m-70) cc_final: 0.6107 (m-70) REVERT: D 277 ASP cc_start: 0.8343 (p0) cc_final: 0.8142 (p0) REVERT: D 379 TRP cc_start: 0.7373 (t60) cc_final: 0.6871 (t60) REVERT: D 411 TYR cc_start: 0.8320 (m-80) cc_final: 0.8075 (m-80) outliers start: 9 outliers final: 5 residues processed: 224 average time/residue: 0.3117 time to fit residues: 96.5811 Evaluate side-chains 142 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain D residue 363 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 40.0000 chunk 42 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 129 optimal weight: 0.2980 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 305 GLN A 389 ASN A 606 ASN ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN C 259 ASN C 287 GLN C 306 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN C 619 GLN C 769 GLN C 830 HIS C 876 HIS ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14639 Z= 0.207 Angle : 0.617 11.941 20007 Z= 0.313 Chirality : 0.041 0.236 2244 Planarity : 0.004 0.057 2361 Dihedral : 14.153 88.316 2486 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.38 % Allowed : 17.47 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.19), residues: 1610 helix: -0.12 (0.20), residues: 582 sheet: -2.40 (0.30), residues: 266 loop : -2.94 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 512 HIS 0.004 0.001 HIS D 260 PHE 0.015 0.001 PHE A 739 TYR 0.017 0.001 TYR C 426 ARG 0.004 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.2673 (OUTLIER) cc_final: 0.2028 (tptp) REVERT: A 521 MET cc_start: 0.6896 (mtp) cc_final: 0.6646 (mtp) REVERT: A 525 MET cc_start: 0.5916 (ttt) cc_final: 0.5601 (tmm) REVERT: A 755 MET cc_start: 0.4081 (tmm) cc_final: 0.2942 (tpt) REVERT: A 760 MET cc_start: 0.4806 (ppp) cc_final: 0.3831 (ppp) REVERT: B 324 HIS cc_start: 0.6507 (m-70) cc_final: 0.6090 (m90) REVERT: C 457 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7691 (pt0) REVERT: C 621 GLU cc_start: 0.8128 (tp30) cc_final: 0.7912 (tp30) REVERT: D 297 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: D 316 GLU cc_start: 0.6523 (tt0) cc_final: 0.6192 (tt0) REVERT: D 379 TRP cc_start: 0.7496 (t60) cc_final: 0.7168 (t60) REVERT: D 428 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6771 (pptt) outliers start: 35 outliers final: 25 residues processed: 185 average time/residue: 0.2747 time to fit residues: 74.7728 Evaluate side-chains 168 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 525 MET Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 428 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 148 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14639 Z= 0.185 Angle : 0.562 11.073 20007 Z= 0.285 Chirality : 0.040 0.212 2244 Planarity : 0.004 0.051 2361 Dihedral : 13.806 89.549 2486 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.15 % Allowed : 18.69 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.21), residues: 1610 helix: 0.74 (0.21), residues: 582 sheet: -2.30 (0.30), residues: 270 loop : -2.68 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 512 HIS 0.003 0.001 HIS D 324 PHE 0.011 0.001 PHE A 459 TYR 0.012 0.001 TYR D 417 ARG 0.003 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 162 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7643 (mtt) REVERT: A 385 MET cc_start: 0.7082 (mmm) cc_final: 0.6786 (mmp) REVERT: A 434 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8909 (tt) REVERT: A 462 LYS cc_start: 0.2745 (OUTLIER) cc_final: 0.2181 (tptp) REVERT: A 760 MET cc_start: 0.4875 (ppp) cc_final: 0.3947 (ppp) REVERT: B 324 HIS cc_start: 0.6460 (m-70) cc_final: 0.6198 (m90) REVERT: B 420 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.7074 (t-90) REVERT: C 457 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7776 (pt0) REVERT: C 523 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6939 (m-80) REVERT: D 297 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: D 301 GLN cc_start: 0.8473 (mt0) cc_final: 0.7673 (pt0) REVERT: D 316 GLU cc_start: 0.6586 (tt0) cc_final: 0.6073 (tt0) REVERT: D 338 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8559 (mm-40) REVERT: D 379 TRP cc_start: 0.7561 (t60) cc_final: 0.6796 (t60) REVERT: D 404 ILE cc_start: 0.4793 (OUTLIER) cc_final: 0.4547 (tp) REVERT: D 428 LYS cc_start: 0.7272 (pptt) cc_final: 0.6694 (pptt) outliers start: 61 outliers final: 41 residues processed: 206 average time/residue: 0.2600 time to fit residues: 79.2620 Evaluate side-chains 191 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 142 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 100 optimal weight: 0.4980 chunk 150 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 142 optimal weight: 0.1980 chunk 42 optimal weight: 8.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN A 557 HIS ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 GLN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14639 Z= 0.249 Angle : 0.599 10.058 20007 Z= 0.304 Chirality : 0.042 0.191 2244 Planarity : 0.004 0.048 2361 Dihedral : 13.750 88.942 2485 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.23 % Allowed : 20.12 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.21), residues: 1610 helix: 0.96 (0.22), residues: 580 sheet: -2.21 (0.30), residues: 264 loop : -2.57 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 908 HIS 0.005 0.001 HIS C 280 PHE 0.018 0.002 PHE A 633 TYR 0.015 0.001 TYR C 426 ARG 0.003 0.000 ARG A 791 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 147 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5638 (OUTLIER) cc_final: 0.5317 (tp) REVERT: A 369 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7580 (mtt) REVERT: A 434 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8916 (tt) REVERT: A 462 LYS cc_start: 0.2567 (OUTLIER) cc_final: 0.2021 (tptp) REVERT: A 521 MET cc_start: 0.7299 (mtp) cc_final: 0.7038 (mtp) REVERT: A 755 MET cc_start: 0.3951 (tmm) cc_final: 0.2991 (ptp) REVERT: A 760 MET cc_start: 0.4872 (ppp) cc_final: 0.3967 (ppp) REVERT: B 324 HIS cc_start: 0.6532 (m-70) cc_final: 0.6319 (m90) REVERT: B 420 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7133 (t-90) REVERT: C 457 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: C 857 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6834 (mm-30) REVERT: D 297 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.7207 (m-10) REVERT: D 379 TRP cc_start: 0.7632 (t60) cc_final: 0.6798 (t60) outliers start: 77 outliers final: 52 residues processed: 205 average time/residue: 0.2148 time to fit residues: 65.8181 Evaluate side-chains 195 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 136 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 8.9990 chunk 90 optimal weight: 0.1980 chunk 2 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 0.0040 chunk 143 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14639 Z= 0.226 Angle : 0.582 9.512 20007 Z= 0.295 Chirality : 0.041 0.186 2244 Planarity : 0.004 0.047 2361 Dihedral : 13.695 86.964 2485 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.17 % Allowed : 20.19 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.21), residues: 1610 helix: 1.10 (0.22), residues: 583 sheet: -2.19 (0.30), residues: 268 loop : -2.49 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 512 HIS 0.003 0.001 HIS D 324 PHE 0.011 0.001 PHE A 739 TYR 0.014 0.001 TYR C 548 ARG 0.003 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 152 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.5304 (tp) REVERT: A 369 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7593 (mtt) REVERT: A 434 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8895 (tt) REVERT: A 462 LYS cc_start: 0.2525 (OUTLIER) cc_final: 0.2028 (tptp) REVERT: A 760 MET cc_start: 0.4887 (ppp) cc_final: 0.4034 (ppp) REVERT: B 420 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.7197 (t-90) REVERT: C 457 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7757 (pt0) REVERT: D 404 ILE cc_start: 0.4824 (OUTLIER) cc_final: 0.4611 (tp) outliers start: 76 outliers final: 59 residues processed: 208 average time/residue: 0.2370 time to fit residues: 73.2423 Evaluate side-chains 202 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 136 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 428 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN D 338 GLN D 381 ASN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14639 Z= 0.386 Angle : 0.696 8.997 20007 Z= 0.354 Chirality : 0.045 0.182 2244 Planarity : 0.004 0.048 2361 Dihedral : 13.885 84.601 2485 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.25 % Allowed : 20.94 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1610 helix: 0.90 (0.22), residues: 576 sheet: -2.23 (0.31), residues: 266 loop : -2.51 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 908 HIS 0.005 0.001 HIS A 782 PHE 0.028 0.002 PHE A 633 TYR 0.014 0.002 TYR C 426 ARG 0.005 0.001 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 140 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5655 (OUTLIER) cc_final: 0.5313 (tp) REVERT: A 369 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7616 (mtt) REVERT: A 462 LYS cc_start: 0.2574 (OUTLIER) cc_final: 0.1824 (tptp) REVERT: A 525 MET cc_start: 0.5272 (tmm) cc_final: 0.5023 (tmm) REVERT: A 760 MET cc_start: 0.5070 (ppp) cc_final: 0.4192 (ppp) REVERT: B 420 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.7162 (t-90) REVERT: C 457 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7759 (pt0) REVERT: D 338 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8696 (tp40) outliers start: 92 outliers final: 68 residues processed: 211 average time/residue: 0.2503 time to fit residues: 78.4970 Evaluate side-chains 206 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 133 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 753 ILE Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 428 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 90 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 0.0070 overall best weight: 1.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN A 549 ASN ** A 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 830 HIS ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14639 Z= 0.180 Angle : 0.590 13.752 20007 Z= 0.293 Chirality : 0.041 0.191 2244 Planarity : 0.004 0.047 2361 Dihedral : 13.698 86.190 2485 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 4.62 % Allowed : 22.57 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.21), residues: 1610 helix: 1.25 (0.22), residues: 582 sheet: -2.08 (0.31), residues: 266 loop : -2.40 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 512 HIS 0.004 0.001 HIS A 281 PHE 0.013 0.001 PHE A 633 TYR 0.018 0.001 TYR C 548 ARG 0.004 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 150 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5606 (OUTLIER) cc_final: 0.5297 (tp) REVERT: A 369 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7096 (mtm) REVERT: A 434 LEU cc_start: 0.9041 (tt) cc_final: 0.8828 (tt) REVERT: A 462 LYS cc_start: 0.2556 (OUTLIER) cc_final: 0.1982 (tptp) REVERT: A 525 MET cc_start: 0.5251 (tmm) cc_final: 0.5039 (tmm) REVERT: A 760 MET cc_start: 0.5121 (ppp) cc_final: 0.4278 (ppp) REVERT: B 420 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.7131 (t-90) REVERT: C 457 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7807 (pt0) REVERT: D 338 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8580 (tp40) outliers start: 68 outliers final: 49 residues processed: 199 average time/residue: 0.2539 time to fit residues: 76.2762 Evaluate side-chains 193 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 139 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 428 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN D 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14639 Z= 0.244 Angle : 0.630 13.850 20007 Z= 0.314 Chirality : 0.042 0.216 2244 Planarity : 0.004 0.046 2361 Dihedral : 13.656 83.325 2484 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 5.17 % Allowed : 23.11 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1610 helix: 1.29 (0.22), residues: 582 sheet: -2.13 (0.30), residues: 274 loop : -2.38 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 512 HIS 0.003 0.001 HIS D 324 PHE 0.013 0.001 PHE A 633 TYR 0.022 0.001 TYR C 548 ARG 0.005 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 142 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5700 (OUTLIER) cc_final: 0.5359 (tp) REVERT: A 369 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7545 (mtt) REVERT: A 462 LYS cc_start: 0.2439 (OUTLIER) cc_final: 0.1997 (tptp) REVERT: A 760 MET cc_start: 0.5116 (ppp) cc_final: 0.4334 (ppp) REVERT: B 420 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.7137 (t-90) REVERT: C 434 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9150 (mp) REVERT: C 457 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: D 316 GLU cc_start: 0.6538 (tt0) cc_final: 0.5716 (tt0) REVERT: D 338 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8592 (tp40) REVERT: D 379 TRP cc_start: 0.7662 (t60) cc_final: 0.7199 (t60) outliers start: 76 outliers final: 59 residues processed: 199 average time/residue: 0.2544 time to fit residues: 76.9662 Evaluate side-chains 203 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 138 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 30.0000 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN D 313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14639 Z= 0.305 Angle : 0.664 12.800 20007 Z= 0.334 Chirality : 0.043 0.217 2244 Planarity : 0.004 0.047 2361 Dihedral : 13.722 82.196 2484 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 5.23 % Allowed : 23.45 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1610 helix: 1.17 (0.22), residues: 580 sheet: -2.07 (0.31), residues: 269 loop : -2.40 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 315 HIS 0.004 0.001 HIS D 324 PHE 0.014 0.002 PHE A 460 TYR 0.021 0.002 TYR C 548 ARG 0.005 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 141 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5715 (OUTLIER) cc_final: 0.5399 (tp) REVERT: A 369 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7576 (mtt) REVERT: A 462 LYS cc_start: 0.2567 (OUTLIER) cc_final: 0.2006 (tptp) REVERT: A 760 MET cc_start: 0.5219 (ppp) cc_final: 0.4405 (ppp) REVERT: B 420 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7168 (t-90) REVERT: C 434 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9148 (mp) REVERT: C 457 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: D 338 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8624 (tp40) REVERT: D 379 TRP cc_start: 0.7686 (t60) cc_final: 0.7210 (t60) outliers start: 77 outliers final: 64 residues processed: 200 average time/residue: 0.2407 time to fit residues: 72.6222 Evaluate side-chains 211 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 141 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 0.0030 chunk 108 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 chunk 151 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN ** A 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14639 Z= 0.155 Angle : 0.595 12.750 20007 Z= 0.293 Chirality : 0.041 0.206 2244 Planarity : 0.004 0.047 2361 Dihedral : 13.599 86.684 2484 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.87 % Allowed : 24.81 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.21), residues: 1610 helix: 1.54 (0.22), residues: 574 sheet: -2.00 (0.30), residues: 277 loop : -2.15 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 512 HIS 0.005 0.001 HIS D 313 PHE 0.011 0.001 PHE A 842 TYR 0.024 0.001 TYR C 548 ARG 0.005 0.000 ARG A 559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 166 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5491 (OUTLIER) cc_final: 0.5185 (tp) REVERT: A 369 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7120 (mtm) REVERT: A 462 LYS cc_start: 0.2479 (OUTLIER) cc_final: 0.2186 (tptp) REVERT: A 724 MET cc_start: 0.2884 (mmm) cc_final: 0.2443 (mmm) REVERT: A 760 MET cc_start: 0.5304 (ppp) cc_final: 0.4723 (ppp) REVERT: B 420 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.7260 (t-90) REVERT: C 434 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9182 (mp) REVERT: D 303 LEU cc_start: 0.8659 (mm) cc_final: 0.8452 (mm) outliers start: 57 outliers final: 41 residues processed: 208 average time/residue: 0.2366 time to fit residues: 74.6770 Evaluate side-chains 195 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 149 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 131 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN ** A 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 GLN D 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.138030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.113698 restraints weight = 37358.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.115808 restraints weight = 33329.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.115676 restraints weight = 27479.399| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14639 Z= 0.172 Angle : 0.608 16.118 20007 Z= 0.298 Chirality : 0.041 0.220 2244 Planarity : 0.004 0.045 2361 Dihedral : 13.548 84.137 2484 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 3.33 % Allowed : 25.97 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1610 helix: 1.62 (0.22), residues: 572 sheet: -1.88 (0.30), residues: 271 loop : -2.13 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 379 HIS 0.004 0.001 HIS D 313 PHE 0.015 0.001 PHE D 263 TYR 0.030 0.001 TYR C 548 ARG 0.005 0.000 ARG A 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2525.98 seconds wall clock time: 49 minutes 8.33 seconds (2948.33 seconds total)