Starting phenix.real_space_refine on Fri Feb 16 01:56:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7v_29825/02_2024/8g7v_29825_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7v_29825/02_2024/8g7v_29825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7v_29825/02_2024/8g7v_29825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7v_29825/02_2024/8g7v_29825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7v_29825/02_2024/8g7v_29825_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7v_29825/02_2024/8g7v_29825_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 48 5.49 5 S 78 5.16 5 C 8762 2.51 5 N 2393 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ASP 562": "OD1" <-> "OD2" 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 ASP 603": "OD1" <-> "OD2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A ASP 802": "OD1" <-> "OD2" Residue "A TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "A PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 372": "OD1" <-> "OD2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C ASP 421": "OD1" <-> "OD2" Residue "C TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 481": "OD1" <-> "OD2" Residue "C ARG 502": "NH1" <-> "NH2" Residue "C ASP 529": "OD1" <-> "OD2" Residue "C ARG 533": "NH1" <-> "NH2" Residue "C ASP 550": "OD1" <-> "OD2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "C GLU 620": "OE1" <-> "OE2" Residue "C TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 627": "OE1" <-> "OE2" Residue "C PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 811": "NH1" <-> "NH2" Residue "C GLU 827": "OE1" <-> "OE2" Residue "C PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 296": "NH1" <-> "NH2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14007 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: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1392 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5005 Classifications: {'peptide': 618} Link IDs: {'PTRANS': 24, 'TRANS': 593} Chain breaks: 4 Chain: "D" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1386 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 501 Unusual residues: {'GTP': 1} Classifications: {'RNA': 22, 'undetermined': 1} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 11} Link IDs: {'rna3p': 21, None: 1} Not linked: pdbres="GTP X 1 " pdbres=" G X 2 " Chain: "Y" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 487 Classifications: {'RNA': 23} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 21} 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 4741 SG CYS A 864 96.663 76.558 85.552 1.00 44.09 S ATOM 4780 SG CYS A 869 93.580 76.262 83.569 1.00 47.18 S ATOM 10817 SG CYS C 810 84.696 25.785 72.262 1.00 61.51 S ATOM 10843 SG CYS C 813 88.128 24.213 72.341 1.00 69.91 S ATOM 11155 SG CYS C 864 88.208 27.375 74.808 1.00 60.77 S ATOM 11194 SG CYS C 869 87.723 27.618 71.176 1.00 66.05 S Time building chain proxies: 7.84, per 1000 atoms: 0.56 Number of scatterers: 14007 At special positions: 0 Unit cell: (119.138, 115.782, 153.537, 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 78 16.00 P 48 15.00 O 2724 8.00 N 2393 7.00 C 8762 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 810 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 864 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 813 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 869 " Number of angles added : 6 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 14 sheets defined 33.3% alpha, 8.9% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 267 through 282 removed outlier: 4.057A pdb=" N THR A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.825A pdb=" N ASN A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) 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 384 through 394 removed outlier: 3.924A pdb=" N ASN A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 434 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 470 through 487 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 507 through 521 removed outlier: 3.753A pdb=" N MET A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 557 removed outlier: 4.163A pdb=" N LYS A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.873A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 601 removed outlier: 3.681A pdb=" N ASP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 592 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 624 removed outlier: 3.615A pdb=" N PHE A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 745 through 770 removed outlier: 3.555A pdb=" N GLU A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 793 removed outlier: 3.695A pdb=" N ARG A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 781 " --> pdb=" O ARG A 777 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 783 " --> pdb=" O LYS A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 840 removed outlier: 3.768A pdb=" N GLU A 840 " --> pdb=" O ALA A 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 837 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 'C' and resid 246 through 256 removed outlier: 3.973A pdb=" N ALA C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Proline residue: C 253 - end of helix removed outlier: 3.924A pdb=" N LYS C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 283 removed outlier: 4.270A pdb=" N LEU C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 314 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 450 Processing helix chain 'C' and resid 470 through 490 Processing helix chain 'C' and resid 493 through 496 No H-bonds generated for 'chain 'C' and resid 493 through 496' Processing helix chain 'C' and resid 507 through 520 Processing helix chain 'C' and resid 530 through 557 removed outlier: 3.564A pdb=" N HIS C 557 " --> pdb=" O ILE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 Processing helix chain 'C' and resid 581 through 601 removed outlier: 3.910A pdb=" N LYS C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 624 Processing helix chain 'C' and resid 637 through 648 Processing helix chain 'C' and resid 747 through 770 removed outlier: 4.083A pdb=" N THR C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 791 Processing helix chain 'C' and resid 838 through 840 No H-bonds generated for 'chain 'C' and resid 838 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 457 through 462 removed outlier: 3.837A pdb=" N PHE A 459 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 740 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 712 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU A 741 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 714 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 631 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR A 715 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 633 " --> pdb=" O TYR A 715 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 892 through 895 removed outlier: 3.627A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 823 through 825 Processing sheet with id= D, first strand: chain 'A' and resid 874 through 878 Processing sheet with id= E, first strand: chain 'B' and resid 280 through 282 Processing sheet with id= F, first strand: chain 'B' and resid 313 through 318 removed outlier: 4.327A pdb=" N VAL B 317 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 376 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 381 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 386 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 414 through 416 removed outlier: 4.257A pdb=" N TRP B 325 " --> pdb=" O TRP B 351 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 260 through 263 removed outlier: 3.801A pdb=" N LEU C 408 " --> pdb=" O PHE C 371 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 457 through 462 removed outlier: 3.736A pdb=" N CYS C 738 " --> pdb=" O GLN C 457 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 892 through 896 removed outlier: 3.672A pdb=" N CYS C 818 " --> pdb=" O LEU C 808 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS C 810 " --> pdb=" O LEU C 816 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU C 816 " --> pdb=" O CYS C 810 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 874 through 876 Processing sheet with id= L, first strand: chain 'D' and resid 280 through 282 removed outlier: 3.564A pdb=" N LEU D 425 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 301 through 303 removed outlier: 4.427A pdb=" N TRP D 325 " --> pdb=" O TRP D 351 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 351 " --> pdb=" O TRP D 325 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 327 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 349 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N CYS D 348 " --> pdb=" O TRP D 360 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 352 " --> pdb=" O GLN D 356 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN D 356 " --> pdb=" O LYS D 352 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 314 through 318 removed outlier: 3.500A pdb=" N TRP D 315 " --> pdb=" O ILE D 378 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 5.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2226 1.32 - 1.44: 4088 1.44 - 1.57: 7893 1.57 - 1.70: 96 1.70 - 1.82: 104 Bond restraints: 14407 Sorted by residual: bond pdb=" C1' GTP X 1 " pdb=" C2' GTP X 1 " ideal model delta sigma weight residual 1.524 1.292 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C1' GTP X 1 " pdb=" O4' GTP X 1 " ideal model delta sigma weight residual 1.410 1.618 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C5 GTP X 1 " pdb=" C6 GTP X 1 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C4 GTP X 1 " pdb=" N3 GTP X 1 " ideal model delta sigma weight residual 1.355 1.493 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C2 GTP X 1 " pdb=" N2 GTP X 1 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 14402 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.87: 494 105.87 - 112.92: 7791 112.92 - 119.97: 5118 119.97 - 127.02: 6018 127.02 - 134.07: 270 Bond angle restraints: 19691 Sorted by residual: angle pdb=" N VAL C 332 " pdb=" CA VAL C 332 " pdb=" C VAL C 332 " ideal model delta sigma weight residual 108.88 120.51 -11.63 2.16e+00 2.14e-01 2.90e+01 angle pdb=" N THR A 881 " pdb=" CA THR A 881 " pdb=" C THR A 881 " ideal model delta sigma weight residual 114.56 108.98 5.58 1.27e+00 6.20e-01 1.93e+01 angle pdb=" N THR B 299 " pdb=" CA THR B 299 " pdb=" C THR B 299 " ideal model delta sigma weight residual 110.80 101.71 9.09 2.13e+00 2.20e-01 1.82e+01 angle pdb=" CA VAL C 332 " pdb=" CB VAL C 332 " pdb=" CG1 VAL C 332 " ideal model delta sigma weight residual 110.40 117.18 -6.78 1.70e+00 3.46e-01 1.59e+01 angle pdb=" C ALA A 733 " pdb=" N ARG A 734 " pdb=" CA ARG A 734 " ideal model delta sigma weight residual 121.54 128.83 -7.29 1.91e+00 2.74e-01 1.46e+01 ... (remaining 19686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.36: 8210 26.36 - 52.72: 434 52.72 - 79.08: 104 79.08 - 105.44: 12 105.44 - 131.80: 2 Dihedral angle restraints: 8762 sinusoidal: 3996 harmonic: 4766 Sorted by residual: dihedral pdb=" C4' GTP X 1 " pdb=" C5' GTP X 1 " pdb=" O5' GTP X 1 " pdb=" PA GTP X 1 " ideal model delta sinusoidal sigma weight residual 260.87 129.08 131.80 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O3B GTP X 1 " pdb=" O3A GTP X 1 " pdb=" PB GTP X 1 " pdb=" PA GTP X 1 " ideal model delta sinusoidal sigma weight residual 291.08 166.30 124.78 1 2.00e+01 2.50e-03 3.77e+01 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 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 8759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1928 0.078 - 0.156: 268 0.156 - 0.234: 19 0.234 - 0.312: 1 0.312 - 0.390: 1 Chirality restraints: 2217 Sorted by residual: chirality pdb=" CA VAL C 332 " pdb=" N VAL C 332 " pdb=" C VAL C 332 " pdb=" CB VAL C 332 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB VAL A 877 " pdb=" CA VAL A 877 " pdb=" CG1 VAL A 877 " pdb=" CG2 VAL A 877 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 875 " pdb=" CA ILE A 875 " pdb=" CG1 ILE A 875 " pdb=" CG2 ILE A 875 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2214 not shown) Planarity restraints: 2330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 332 " -0.100 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO C 333 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 712 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C VAL C 712 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL C 712 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE C 713 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO A 382 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " 0.041 5.00e-02 4.00e+02 ... (remaining 2327 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2934 2.78 - 3.31: 12404 3.31 - 3.84: 23313 3.84 - 4.37: 25911 4.37 - 4.90: 43851 Nonbonded interactions: 108413 Sorted by model distance: nonbonded pdb=" CD LYS A 806 " pdb=" OD1 ASP A 896 " model vdw 2.246 3.440 nonbonded pdb=" O SER B 300 " pdb=" OG SER B 300 " model vdw 2.286 2.440 nonbonded pdb=" O LEU C 538 " pdb=" OG1 THR C 542 " model vdw 2.301 2.440 nonbonded pdb=" OG SER D 300 " pdb=" O LEU D 416 " model vdw 2.316 2.440 nonbonded pdb=" O LEU C 597 " pdb=" OG SER C 601 " model vdw 2.318 2.440 ... (remaining 108408 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 845 or resid 858 through 921 or resid 1001)) selection = (chain 'C' and (resid 241 through 921 or resid 1001)) } ncs_group { reference = (chain 'B' and (resid 252 through 335 or (resid 336 and (name N or name CA or na \ me C or name O or name CB )) or resid 337 through 382 or (resid 383 through 384 \ and (name N or name CA or name C or name O or name CB )) or resid 385 through 43 \ 0)) selection = (chain 'D' and (resid 252 through 394 or (resid 395 through 399 and (name N or n \ ame CA or name C or name O or name CB )) or resid 400 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: 0.010 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.810 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 43.740 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.007 0.232 14407 Z= 0.451 Angle : 0.849 12.952 19691 Z= 0.458 Chirality : 0.053 0.390 2217 Planarity : 0.007 0.151 2330 Dihedral : 16.749 131.797 5654 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.42 % Allowed : 9.09 % Favored : 90.49 % 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: -4.07 (0.16), residues: 1595 helix: -2.06 (0.17), residues: 569 sheet: -2.89 (0.28), residues: 253 loop : -3.13 (0.17), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 379 HIS 0.010 0.002 HIS C 691 PHE 0.024 0.002 PHE A 853 TYR 0.022 0.002 TYR C 879 ARG 0.004 0.001 ARG C 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 1.541 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: A 385 MET cc_start: 0.8800 (mmm) cc_final: 0.8510 (mtp) REVERT: A 387 MET cc_start: 0.8649 (mmm) cc_final: 0.8386 (mmp) REVERT: A 573 ASN cc_start: 0.8260 (t0) cc_final: 0.8022 (t0) REVERT: A 828 GLU cc_start: 0.7165 (mp0) cc_final: 0.6905 (mp0) REVERT: A 890 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7497 (tm-30) REVERT: B 266 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7758 (mttm) REVERT: B 400 TYR cc_start: 0.6077 (t80) cc_final: 0.5526 (t80) REVERT: C 300 ILE cc_start: 0.9142 (mm) cc_final: 0.8901 (mt) REVERT: C 419 ASN cc_start: 0.8873 (p0) cc_final: 0.8617 (p0) REVERT: C 598 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8103 (mt-10) REVERT: C 624 LEU cc_start: 0.8703 (tt) cc_final: 0.8358 (mp) REVERT: D 357 LEU cc_start: 0.5726 (tp) cc_final: 0.5306 (pp) outliers start: 6 outliers final: 5 residues processed: 204 average time/residue: 0.2923 time to fit residues: 85.1912 Evaluate side-chains 138 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain D residue 282 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 317 HIS A 336 GLN A 353 ASN A 375 HIS A 393 GLN A 404 GLN A 445 ASN A 595 GLN A 623 HIS A 645 ASN A 805 ASN B 301 GLN B 338 GLN B 394 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN C 349 GLN C 354 ASN C 573 ASN C 595 GLN C 692 ASN C 830 HIS D 288 GLN D 321 ASN D 381 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14407 Z= 0.264 Angle : 0.617 13.679 19691 Z= 0.312 Chirality : 0.042 0.220 2217 Planarity : 0.005 0.101 2330 Dihedral : 13.653 101.919 2449 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.57 % Allowed : 15.20 % Favored : 82.23 % 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: 1595 helix: -0.25 (0.21), residues: 571 sheet: -2.47 (0.30), residues: 251 loop : -2.77 (0.19), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 379 HIS 0.006 0.001 HIS A 623 PHE 0.024 0.002 PHE C 471 TYR 0.017 0.002 TYR C 541 ARG 0.003 0.000 ARG C 533 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8865 (mmm) cc_final: 0.8484 (mtp) REVERT: A 573 ASN cc_start: 0.8253 (t0) cc_final: 0.8014 (t0) REVERT: A 828 GLU cc_start: 0.7385 (mp0) cc_final: 0.7065 (mp0) REVERT: B 337 ASP cc_start: 0.7991 (m-30) cc_final: 0.7744 (m-30) REVERT: B 379 TRP cc_start: 0.6807 (t-100) cc_final: 0.6541 (t-100) REVERT: C 419 ASN cc_start: 0.8951 (p0) cc_final: 0.8481 (p0) REVERT: C 560 MET cc_start: 0.8221 (mmt) cc_final: 0.8020 (mmt) REVERT: C 598 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8109 (mt-10) REVERT: C 624 LEU cc_start: 0.8658 (tt) cc_final: 0.8437 (mp) REVERT: C 716 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7425 (tm-30) outliers start: 37 outliers final: 26 residues processed: 168 average time/residue: 0.2588 time to fit residues: 66.2950 Evaluate side-chains 149 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 148 optimal weight: 40.0000 chunk 160 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14407 Z= 0.363 Angle : 0.668 15.587 19691 Z= 0.334 Chirality : 0.044 0.246 2217 Planarity : 0.005 0.098 2330 Dihedral : 13.440 90.766 2448 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 3.96 % Allowed : 17.28 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.20), residues: 1595 helix: 0.39 (0.22), residues: 568 sheet: -2.49 (0.30), residues: 262 loop : -2.59 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 315 HIS 0.006 0.001 HIS A 281 PHE 0.022 0.002 PHE C 471 TYR 0.018 0.002 TYR C 313 ARG 0.004 0.000 ARG C 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 134 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8862 (mmm) cc_final: 0.8538 (mtp) REVERT: A 573 ASN cc_start: 0.8250 (t0) cc_final: 0.7970 (t0) REVERT: A 828 GLU cc_start: 0.7372 (mp0) cc_final: 0.7058 (mp0) REVERT: B 312 LYS cc_start: 0.7265 (mmtm) cc_final: 0.6986 (ptpp) REVERT: B 337 ASP cc_start: 0.8057 (m-30) cc_final: 0.7803 (m-30) REVERT: B 400 TYR cc_start: 0.6277 (t80) cc_final: 0.5816 (t80) REVERT: C 419 ASN cc_start: 0.8968 (p0) cc_final: 0.8504 (p0) REVERT: C 598 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8121 (mp0) REVERT: C 716 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7273 (tm-30) outliers start: 57 outliers final: 45 residues processed: 181 average time/residue: 0.2351 time to fit residues: 65.7545 Evaluate side-chains 164 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 119 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 616 PHE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 16 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 148 optimal weight: 40.0000 chunk 157 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14407 Z= 0.179 Angle : 0.548 12.315 19691 Z= 0.275 Chirality : 0.041 0.254 2217 Planarity : 0.004 0.086 2330 Dihedral : 13.206 90.057 2448 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.75 % Allowed : 19.22 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.21), residues: 1595 helix: 0.94 (0.22), residues: 570 sheet: -2.11 (0.32), residues: 255 loop : -2.49 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 315 HIS 0.003 0.001 HIS C 281 PHE 0.027 0.001 PHE C 471 TYR 0.024 0.001 TYR C 313 ARG 0.002 0.000 ARG C 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 144 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8872 (mmm) cc_final: 0.8429 (mtp) REVERT: A 434 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9075 (tt) REVERT: A 573 ASN cc_start: 0.8266 (t0) cc_final: 0.8016 (t0) REVERT: A 828 GLU cc_start: 0.7387 (mp0) cc_final: 0.7084 (mp0) REVERT: B 257 TRP cc_start: 0.5742 (m100) cc_final: 0.5407 (m100) REVERT: B 337 ASP cc_start: 0.8002 (m-30) cc_final: 0.7744 (m-30) REVERT: C 598 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8118 (mp0) REVERT: C 716 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7260 (tm-30) REVERT: C 819 TYR cc_start: 0.7793 (m-80) cc_final: 0.7554 (m-80) outliers start: 54 outliers final: 43 residues processed: 188 average time/residue: 0.2272 time to fit residues: 66.6085 Evaluate side-chains 172 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 141 optimal weight: 0.0980 chunk 39 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN B 301 GLN B 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14407 Z= 0.245 Angle : 0.599 13.101 19691 Z= 0.296 Chirality : 0.042 0.254 2217 Planarity : 0.004 0.084 2330 Dihedral : 13.174 88.899 2448 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 4.23 % Allowed : 20.47 % Favored : 75.29 % 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: -1.55 (0.21), residues: 1595 helix: 1.08 (0.22), residues: 572 sheet: -2.11 (0.32), residues: 258 loop : -2.36 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 315 HIS 0.003 0.001 HIS A 281 PHE 0.029 0.001 PHE C 471 TYR 0.020 0.001 TYR C 313 ARG 0.003 0.000 ARG C 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 131 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8850 (mmm) cc_final: 0.8472 (mtp) REVERT: A 434 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9022 (tt) REVERT: A 525 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7082 (tmm) REVERT: A 828 GLU cc_start: 0.7388 (mp0) cc_final: 0.7062 (mp0) REVERT: B 337 ASP cc_start: 0.8081 (m-30) cc_final: 0.7803 (m-30) REVERT: C 479 MET cc_start: 0.8992 (mmm) cc_final: 0.8685 (mmt) REVERT: C 598 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8151 (mp0) REVERT: C 716 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7136 (tm-30) REVERT: C 819 TYR cc_start: 0.7783 (m-80) cc_final: 0.7557 (m-80) outliers start: 61 outliers final: 56 residues processed: 179 average time/residue: 0.2280 time to fit residues: 64.7673 Evaluate side-chains 179 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 121 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 616 PHE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain C residue 906 SER Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.0070 chunk 82 optimal weight: 0.8980 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN B 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14407 Z= 0.155 Angle : 0.539 11.232 19691 Z= 0.268 Chirality : 0.040 0.220 2217 Planarity : 0.004 0.077 2330 Dihedral : 13.036 90.961 2448 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.54 % Allowed : 21.58 % Favored : 74.88 % 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: -1.27 (0.21), residues: 1595 helix: 1.31 (0.22), residues: 572 sheet: -1.83 (0.34), residues: 242 loop : -2.25 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 315 HIS 0.002 0.001 HIS C 876 PHE 0.035 0.001 PHE C 471 TYR 0.017 0.001 TYR C 313 ARG 0.002 0.000 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 135 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8999 (tt) REVERT: A 828 GLU cc_start: 0.7407 (mp0) cc_final: 0.7081 (mp0) REVERT: B 337 ASP cc_start: 0.8070 (m-30) cc_final: 0.7781 (m-30) REVERT: C 598 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8163 (mp0) REVERT: C 716 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7158 (tm-30) outliers start: 51 outliers final: 39 residues processed: 173 average time/residue: 0.2261 time to fit residues: 61.3515 Evaluate side-chains 164 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 124 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 157 optimal weight: 50.0000 chunk 98 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN B 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14407 Z= 0.337 Angle : 0.653 14.267 19691 Z= 0.322 Chirality : 0.044 0.211 2217 Planarity : 0.004 0.081 2330 Dihedral : 13.107 88.962 2447 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 4.58 % Allowed : 21.24 % Favored : 74.18 % 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: -1.39 (0.21), residues: 1595 helix: 1.13 (0.22), residues: 575 sheet: -1.94 (0.33), residues: 258 loop : -2.24 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 315 HIS 0.004 0.001 HIS C 876 PHE 0.018 0.002 PHE A 853 TYR 0.017 0.002 TYR C 313 ARG 0.009 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 123 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8790 (mmm) cc_final: 0.8390 (mtp) REVERT: A 434 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9007 (tt) REVERT: A 525 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7108 (tmm) REVERT: A 828 GLU cc_start: 0.7413 (mp0) cc_final: 0.7074 (mp0) REVERT: B 337 ASP cc_start: 0.8158 (m-30) cc_final: 0.7864 (m-30) REVERT: C 560 MET cc_start: 0.8480 (tpp) cc_final: 0.8115 (mmt) REVERT: C 598 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8134 (mp0) REVERT: C 716 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7142 (tm-30) REVERT: C 872 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8340 (p0) outliers start: 66 outliers final: 55 residues processed: 177 average time/residue: 0.2247 time to fit residues: 63.8661 Evaluate side-chains 173 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 115 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 616 PHE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 872 ASP Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 14 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 150 optimal weight: 0.0010 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14407 Z= 0.138 Angle : 0.546 10.547 19691 Z= 0.270 Chirality : 0.041 0.228 2217 Planarity : 0.004 0.073 2330 Dihedral : 12.921 91.143 2447 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.75 % Allowed : 22.14 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1595 helix: 1.43 (0.22), residues: 572 sheet: -1.73 (0.34), residues: 254 loop : -2.14 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 315 HIS 0.003 0.001 HIS C 281 PHE 0.024 0.001 PHE C 471 TYR 0.027 0.001 TYR B 400 ARG 0.004 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 135 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7085 (tmm) REVERT: A 828 GLU cc_start: 0.7396 (mp0) cc_final: 0.7056 (mp0) REVERT: B 337 ASP cc_start: 0.8097 (m-30) cc_final: 0.7805 (m-30) REVERT: B 417 TYR cc_start: 0.8204 (t80) cc_final: 0.7896 (t80) REVERT: C 560 MET cc_start: 0.8328 (tpp) cc_final: 0.7947 (mmt) REVERT: C 598 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8158 (mt-10) REVERT: C 716 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7138 (tm-30) outliers start: 54 outliers final: 43 residues processed: 178 average time/residue: 0.2308 time to fit residues: 64.2883 Evaluate side-chains 171 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 127 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 10.0000 chunk 146 optimal weight: 0.1980 chunk 150 optimal weight: 40.0000 chunk 88 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 145 optimal weight: 50.0000 chunk 96 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14407 Z= 0.211 Angle : 0.588 11.690 19691 Z= 0.286 Chirality : 0.042 0.218 2217 Planarity : 0.004 0.072 2330 Dihedral : 12.900 89.859 2447 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 3.96 % Allowed : 22.28 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.22), residues: 1595 helix: 1.37 (0.22), residues: 573 sheet: -1.71 (0.34), residues: 254 loop : -2.13 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 646 HIS 0.003 0.001 HIS C 876 PHE 0.023 0.001 PHE C 471 TYR 0.026 0.001 TYR B 400 ARG 0.004 0.000 ARG C 824 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 124 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7011 (tmm) REVERT: A 828 GLU cc_start: 0.7425 (mp0) cc_final: 0.7078 (mp0) REVERT: B 337 ASP cc_start: 0.8144 (m-30) cc_final: 0.7842 (m-30) REVERT: B 417 TYR cc_start: 0.8186 (t80) cc_final: 0.7838 (t80) REVERT: C 560 MET cc_start: 0.8345 (tpp) cc_final: 0.7932 (mmt) REVERT: C 598 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8184 (mt-10) REVERT: C 716 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7112 (tm-30) REVERT: C 872 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8279 (p0) outliers start: 57 outliers final: 51 residues processed: 169 average time/residue: 0.2237 time to fit residues: 59.8393 Evaluate side-chains 172 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 119 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 872 ASP Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 107 optimal weight: 0.0980 chunk 162 optimal weight: 10.0000 chunk 149 optimal weight: 40.0000 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 0.0570 chunk 102 optimal weight: 7.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14407 Z= 0.144 Angle : 0.563 10.356 19691 Z= 0.275 Chirality : 0.041 0.222 2217 Planarity : 0.004 0.067 2330 Dihedral : 12.763 90.308 2447 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.54 % Allowed : 22.90 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1595 helix: 1.53 (0.23), residues: 572 sheet: -1.46 (0.35), residues: 249 loop : -2.05 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 646 HIS 0.003 0.000 HIS C 281 PHE 0.024 0.001 PHE C 471 TYR 0.028 0.001 TYR B 400 ARG 0.003 0.000 ARG C 824 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 137 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.7022 (tmm) REVERT: A 755 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7808 (pmm) REVERT: A 828 GLU cc_start: 0.7386 (mp0) cc_final: 0.7047 (mp0) REVERT: B 316 GLU cc_start: 0.4944 (tp30) cc_final: 0.4430 (tp30) REVERT: B 417 TYR cc_start: 0.8103 (t80) cc_final: 0.7801 (t80) REVERT: C 419 ASN cc_start: 0.8829 (p0) cc_final: 0.8604 (p0) REVERT: C 560 MET cc_start: 0.8306 (tpp) cc_final: 0.7910 (mmt) REVERT: C 598 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8194 (mt-10) REVERT: C 716 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 896 ASP cc_start: 0.7867 (m-30) cc_final: 0.7440 (m-30) outliers start: 51 outliers final: 49 residues processed: 177 average time/residue: 0.2405 time to fit residues: 65.7996 Evaluate side-chains 180 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 129 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.120359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096392 restraints weight = 36145.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095444 restraints weight = 29545.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.096344 restraints weight = 25582.043| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14407 Z= 0.260 Angle : 0.632 13.338 19691 Z= 0.306 Chirality : 0.043 0.216 2217 Planarity : 0.004 0.069 2330 Dihedral : 12.815 88.444 2447 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.89 % Allowed : 22.90 % Favored : 73.21 % 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: -1.09 (0.22), residues: 1595 helix: 1.39 (0.22), residues: 572 sheet: -1.66 (0.34), residues: 260 loop : -2.10 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 646 HIS 0.004 0.001 HIS C 876 PHE 0.021 0.001 PHE C 471 TYR 0.028 0.002 TYR B 400 ARG 0.004 0.000 ARG B 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2476.83 seconds wall clock time: 46 minutes 25.84 seconds (2785.84 seconds total)