Starting phenix.real_space_refine on Sat Feb 17 17:38:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsn_22458/02_2024/7jsn_22458_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsn_22458/02_2024/7jsn_22458.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsn_22458/02_2024/7jsn_22458_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsn_22458/02_2024/7jsn_22458_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsn_22458/02_2024/7jsn_22458_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsn_22458/02_2024/7jsn_22458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsn_22458/02_2024/7jsn_22458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsn_22458/02_2024/7jsn_22458_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsn_22458/02_2024/7jsn_22458_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 8 5.49 5 Mg 2 5.21 5 S 141 5.16 5 C 12382 2.51 5 N 3258 2.21 5 O 3645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B ARG 799": "NH1" <-> "NH2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 172": "NH1" <-> "NH2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "D ARG 15": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19438 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6707 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 820, 6703 Classifications: {'peptide': 820} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 788} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 820, 6703 Classifications: {'peptide': 820} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 788} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 6851 Chain: "B" Number of atoms: 6532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6532 Classifications: {'peptide': 806} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 774} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2464 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 310} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "F" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2451 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 310} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 551 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 551 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 1, ' ZN': 1, 'VDN': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 1, ' ZN': 1, 'VDN': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A 345 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 345 " occ=0.50 Time building chain proxies: 11.84, per 1000 atoms: 0.61 Number of scatterers: 19438 At special positions: 0 Unit cell: (165.75, 149.6, 146.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 141 16.00 P 8 15.00 Mg 2 11.99 O 3645 8.00 N 3258 7.00 C 12382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.52 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 599 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 563 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 561 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 597 " 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4562 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 7 sheets defined 45.6% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 60 through 67 removed outlier: 4.244A pdb=" N ASP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.627A pdb=" N LYS A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 166 through 169 No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 216 through 219 No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.510A pdb=" N HIS A 226 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR A 229 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 241 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 247 " --> pdb=" O TRP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 262 Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.518A pdb=" N TRP A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Proline residue: A 293 - end of helix No H-bonds generated for 'chain 'A' and resid 288 through 295' Processing helix chain 'A' and resid 347 through 353 removed outlier: 3.790A pdb=" N ALA A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN A 352 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 353 " --> pdb=" O TYR A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 353' Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 414 through 453 removed outlier: 4.143A pdb=" N LEU A 419 " --> pdb=" O MET A 415 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASN A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) Proline residue: A 434 - end of helix removed outlier: 3.594A pdb=" N GLU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 474 No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.661A pdb=" N VAL A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 535 No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.631A pdb=" N ASN A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 567 " --> pdb=" O HIS A 563 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 568 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 608 through 613 removed outlier: 3.644A pdb=" N MET A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 626 through 640 removed outlier: 3.591A pdb=" N HIS A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 668 removed outlier: 3.562A pdb=" N ILE A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 679 through 688 removed outlier: 3.549A pdb=" N SER A 688 " --> pdb=" O ILE A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 702 Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.966A pdb=" N MET A 712 " --> pdb=" O LYS A 708 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 714 " --> pdb=" O ILE A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 725 Processing helix chain 'A' and resid 728 through 751 removed outlier: 4.512A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A 741 " --> pdb=" O LEU A 737 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A 742 " --> pdb=" O VAL A 738 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 747 " --> pdb=" O TRP A 743 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 748 " --> pdb=" O GLU A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 779 removed outlier: 5.122A pdb=" N ASP A 767 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 769 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Proline residue: A 770 - end of helix removed outlier: 4.335A pdb=" N PHE A 776 " --> pdb=" O GLN A 773 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE A 777 " --> pdb=" O VAL A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 791 removed outlier: 3.575A pdb=" N SER A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 826 removed outlier: 3.509A pdb=" N GLY A 801 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 823 " --> pdb=" O LYS A 819 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 824 " --> pdb=" O MET A 820 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 825 " --> pdb=" O LYS A 821 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 60 removed outlier: 3.778A pdb=" N GLU B 55 " --> pdb=" O CYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.698A pdb=" N VAL B 76 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.776A pdb=" N LEU B 167 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 163 through 168' Processing helix chain 'B' and resid 205 through 212 removed outlier: 3.773A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 246 removed outlier: 3.818A pdb=" N LEU B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG B 235 " --> pdb=" O CYS B 231 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 245 " --> pdb=" O TRP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.831A pdb=" N HIS B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 344 through 350 removed outlier: 3.782A pdb=" N ALA B 349 " --> pdb=" O PRO B 345 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 412 through 456 removed outlier: 3.906A pdb=" N LEU B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR B 422 " --> pdb=" O MET B 418 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASN B 431 " --> pdb=" O TRP B 427 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B 436 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 482 through 492 removed outlier: 3.749A pdb=" N LYS B 487 " --> pdb=" O ASP B 483 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 526 removed outlier: 3.517A pdb=" N TYR B 524 " --> pdb=" O GLY B 520 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 533 No H-bonds generated for 'chain 'B' and resid 530 through 533' Processing helix chain 'B' and resid 537 through 550 removed outlier: 3.778A pdb=" N VAL B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 575 removed outlier: 3.638A pdb=" N ALA B 566 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 594 removed outlier: 3.644A pdb=" N ALA B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 612 removed outlier: 3.556A pdb=" N MET B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 619 No H-bonds generated for 'chain 'B' and resid 616 through 619' Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.660A pdb=" N HIS B 628 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 632 " --> pdb=" O HIS B 628 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 667 removed outlier: 3.836A pdb=" N ASP B 661 " --> pdb=" O ILE B 657 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 662 " --> pdb=" O HIS B 658 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 removed outlier: 3.815A pdb=" N LYS B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 688 removed outlier: 3.680A pdb=" N ILE B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 687 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 699 removed outlier: 3.622A pdb=" N GLU B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 718 removed outlier: 3.536A pdb=" N ILE B 708 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET B 712 " --> pdb=" O ILE B 708 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 722 No H-bonds generated for 'chain 'B' and resid 720 through 722' Processing helix chain 'B' and resid 729 through 750 removed outlier: 4.369A pdb=" N LEU B 734 " --> pdb=" O SER B 730 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 759 No H-bonds generated for 'chain 'B' and resid 757 through 759' Processing helix chain 'B' and resid 767 through 777 removed outlier: 3.764A pdb=" N VAL B 772 " --> pdb=" O PRO B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 789 removed outlier: 3.654A pdb=" N TYR B 783 " --> pdb=" O CYS B 779 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 823 removed outlier: 3.630A pdb=" N GLU B 823 " --> pdb=" O LYS B 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 52 Processing helix chain 'E' and resid 61 through 64 No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 67 through 87 removed outlier: 3.981A pdb=" N ILE E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 78 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 85 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 109 removed outlier: 4.512A pdb=" N ASP E 98 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET E 106 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA E 107 " --> pdb=" O MET E 104 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR E 109 " --> pdb=" O MET E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 128 removed outlier: 3.854A pdb=" N GLN E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS E 128 " --> pdb=" O GLN E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 removed outlier: 3.590A pdb=" N ALA E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 151 removed outlier: 4.307A pdb=" N GLY E 149 " --> pdb=" O ASP E 146 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR E 151 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 201 through 210 removed outlier: 4.457A pdb=" N LYS E 205 " --> pdb=" O SER E 202 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 208 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.653A pdb=" N MET E 243 " --> pdb=" O MET E 239 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS E 244 " --> pdb=" O HIS E 240 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 267 through 273 Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 292 through 306 removed outlier: 4.733A pdb=" N LEU E 306 " --> pdb=" O GLN E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 341 Processing helix chain 'F' and resid 42 through 50 removed outlier: 3.599A pdb=" N VAL F 46 " --> pdb=" O LYS F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 86 removed outlier: 5.193A pdb=" N ILE F 66 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER F 76 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE F 80 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR F 85 " --> pdb=" O ARG F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 106 removed outlier: 4.185A pdb=" N ALA F 100 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 127 removed outlier: 3.640A pdb=" N ILE F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 147 through 159 removed outlier: 4.666A pdb=" N LEU F 152 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER F 153 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU F 156 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 170 No H-bonds generated for 'chain 'F' and resid 167 through 170' Processing helix chain 'F' and resid 202 through 211 removed outlier: 3.579A pdb=" N HIS F 209 " --> pdb=" O LYS F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.575A pdb=" N SER F 248 " --> pdb=" O HIS F 244 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE F 249 " --> pdb=" O LEU F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 273 Processing helix chain 'F' and resid 294 through 304 removed outlier: 4.047A pdb=" N TYR F 298 " --> pdb=" O GLU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 341 removed outlier: 3.995A pdb=" N ASP F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA F 334 " --> pdb=" O PHE F 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 67 No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.777A pdb=" N ALA C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 67 No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing sheet with id= A, first strand: chain 'A' and resid 105 through 112 removed outlier: 6.788A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR A 99 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 182 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILE A 191 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER A 180 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET A 193 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A 178 " --> pdb=" O MET A 193 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 177 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.557A pdb=" N VAL A 385 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 274 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS A 317 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 320 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 330 " --> pdb=" O ASP A 320 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 108 removed outlier: 4.006A pdb=" N MET B 191 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR B 97 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 187 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 12.619A pdb=" N GLN B 99 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 15.146A pdb=" N ASP B 185 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 180 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL B 189 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET B 191 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 176 " --> pdb=" O MET B 191 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 328 through 330 removed outlier: 3.641A pdb=" N ASP B 318 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 316 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL B 316 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 275 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP B 318 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR B 273 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 388 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL B 398 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET B 386 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR B 400 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 384 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 383 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 385 " --> pdb=" O CYS B 355 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.505A pdb=" N LEU B 94 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N PHE B 111 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 316 through 319 removed outlier: 4.289A pdb=" N TYR E 316 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS E 318 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 264 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS E 31 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE E 218 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU E 33 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N CYS E 220 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU E 35 " --> pdb=" O CYS E 220 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ALA E 222 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU E 32 " --> pdb=" O ASN E 191 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG E 193 " --> pdb=" O LEU E 32 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU E 34 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE E 195 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLY E 36 " --> pdb=" O PHE E 195 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 316 through 319 removed outlier: 4.134A pdb=" N TYR F 316 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA F 216 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 33 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP F 196 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE F 181 " --> pdb=" O ASP F 196 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.14 Time building geometry restraints manager: 7.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3288 1.30 - 1.43: 5098 1.43 - 1.56: 11230 1.56 - 1.68: 17 1.68 - 1.81: 232 Bond restraints: 19865 Sorted by residual: bond pdb=" O2P 35G A 905 " pdb=" P 35G A 905 " ideal model delta sigma weight residual 1.648 1.456 0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" O2P 35G B 905 " pdb=" P 35G B 905 " ideal model delta sigma weight residual 1.648 1.456 0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" O1P 35G B 905 " pdb=" P 35G B 905 " ideal model delta sigma weight residual 1.461 1.644 -0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" O1P 35G A 905 " pdb=" P 35G A 905 " ideal model delta sigma weight residual 1.461 1.642 -0.181 2.00e-02 2.50e+03 8.15e+01 bond pdb=" N VAL B 778 " pdb=" CA VAL B 778 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.71e+00 ... (remaining 19860 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.85: 570 106.85 - 113.89: 11217 113.89 - 120.92: 9553 120.92 - 127.95: 5380 127.95 - 134.98: 168 Bond angle restraints: 26888 Sorted by residual: angle pdb=" N ASN A 462 " pdb=" CA ASN A 462 " pdb=" C ASN A 462 " ideal model delta sigma weight residual 111.28 119.55 -8.27 1.09e+00 8.42e-01 5.76e+01 angle pdb=" N MET B 712 " pdb=" CA MET B 712 " pdb=" C MET B 712 " ideal model delta sigma weight residual 113.43 106.61 6.82 1.26e+00 6.30e-01 2.93e+01 angle pdb=" N VAL A 195 " pdb=" CA VAL A 195 " pdb=" C VAL A 195 " ideal model delta sigma weight residual 108.11 115.62 -7.51 1.40e+00 5.10e-01 2.88e+01 angle pdb=" CA CYS B 92 " pdb=" C CYS B 92 " pdb=" O CYS B 92 " ideal model delta sigma weight residual 121.45 116.34 5.11 1.07e+00 8.73e-01 2.28e+01 angle pdb=" CA ASP A 461 " pdb=" CB ASP A 461 " pdb=" CG ASP A 461 " ideal model delta sigma weight residual 112.60 117.10 -4.50 1.00e+00 1.00e+00 2.03e+01 ... (remaining 26883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.37: 11654 28.37 - 56.74: 280 56.74 - 85.12: 23 85.12 - 113.49: 3 113.49 - 141.86: 2 Dihedral angle restraints: 11962 sinusoidal: 4921 harmonic: 7041 Sorted by residual: dihedral pdb=" C4' GTP E 351 " pdb=" C5' GTP E 351 " pdb=" O5' GTP E 351 " pdb=" PA GTP E 351 " ideal model delta sinusoidal sigma weight residual 260.87 119.01 141.86 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" C4' GTP F 351 " pdb=" C5' GTP F 351 " pdb=" O5' GTP F 351 " pdb=" PA GTP F 351 " ideal model delta sinusoidal sigma weight residual 260.87 131.97 128.90 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" C8 GTP F 351 " pdb=" C1' GTP F 351 " pdb=" N9 GTP F 351 " pdb=" O4' GTP F 351 " ideal model delta sinusoidal sigma weight residual 104.59 -3.40 107.99 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 11959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2575 0.066 - 0.132: 346 0.132 - 0.199: 23 0.199 - 0.265: 2 0.265 - 0.331: 3 Chirality restraints: 2949 Sorted by residual: chirality pdb=" P 35G A 905 " pdb=" O2P 35G A 905 " pdb=" O3' 35G A 905 " pdb=" O5' 35G A 905 " both_signs ideal model delta sigma weight residual True 3.39 -3.06 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" P 35G B 905 " pdb=" O2P 35G B 905 " pdb=" O3' 35G B 905 " pdb=" O5' 35G B 905 " both_signs ideal model delta sigma weight residual True 3.39 -3.07 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ARG B 676 " pdb=" N ARG B 676 " pdb=" C ARG B 676 " pdb=" CB ARG B 676 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 2946 not shown) Planarity restraints: 3440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 21 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C LYS A 21 " 0.059 2.00e-02 2.50e+03 pdb=" O LYS A 21 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN A 22 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 28 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B 29 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 29 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 29 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 62 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C CYS F 62 " 0.033 2.00e-02 2.50e+03 pdb=" O CYS F 62 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU F 63 " -0.011 2.00e-02 2.50e+03 ... (remaining 3437 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 117 2.57 - 3.16: 16007 3.16 - 3.74: 26934 3.74 - 4.32: 36940 4.32 - 4.90: 62366 Nonbonded interactions: 142364 Sorted by model distance: nonbonded pdb=" OD2 ASP B 598 " pdb="ZN ZN B 902 " model vdw 1.992 2.230 nonbonded pdb=" OD2 ASP A 600 " pdb="ZN ZN A 902 " model vdw 2.007 2.230 nonbonded pdb=" NZ LYS A 223 " pdb=" O GLN B 67 " model vdw 2.214 2.520 nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A 903 " model vdw 2.220 2.170 nonbonded pdb=" O GLU A 642 " pdb=" OG SER A 643 " model vdw 2.235 2.440 ... (remaining 142359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and ((resid 27 through 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 through 256 or (resid 257 and (name N or name CA or na \ me C or name O or name CB )) or resid 258 through 259 or (resid 260 and (name N \ or name CA or name C or name O or name CB )) or resid 261 through 266 or (resid \ 267 and (name N or name CA or name C or name O or name CB )) or resid 268 throug \ h 288 or (resid 289 and (name N or name CA or name C or name O or name CB )) or \ resid 290 through 342 or resid 351)) selection = (chain 'F' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 342 or resid 351)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.870 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 54.800 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.110 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.005 0.192 19865 Z= 0.345 Angle : 0.644 8.349 26888 Z= 0.385 Chirality : 0.046 0.331 2949 Planarity : 0.004 0.048 3440 Dihedral : 12.551 141.859 7400 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.05 % Allowed : 6.21 % Favored : 93.75 % 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: -1.78 (0.16), residues: 2391 helix: -0.84 (0.16), residues: 1069 sheet: -0.05 (0.36), residues: 202 loop : -1.68 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 697 HIS 0.004 0.001 HIS B 597 PHE 0.014 0.001 PHE B 215 TYR 0.024 0.001 TYR B 672 ARG 0.004 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8602 (m-40) cc_final: 0.8378 (m-40) REVERT: A 444 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7134 (tm-30) REVERT: A 464 GLU cc_start: 0.7922 (tt0) cc_final: 0.7622 (tt0) REVERT: A 820 MET cc_start: 0.7783 (tmm) cc_final: 0.7567 (tmm) REVERT: E 119 MET cc_start: 0.7494 (ttm) cc_final: 0.7267 (ttm) REVERT: E 146 ASP cc_start: 0.7332 (t0) cc_final: 0.7122 (t70) REVERT: E 182 GLU cc_start: 0.7509 (mp0) cc_final: 0.7137 (mp0) REVERT: E 210 CYS cc_start: 0.7375 (m) cc_final: 0.6935 (p) REVERT: F 106 MET cc_start: 0.7976 (ppp) cc_final: 0.7581 (ppp) REVERT: F 308 MET cc_start: 0.7931 (tmm) cc_final: 0.7724 (tmm) REVERT: C 74 ASN cc_start: 0.8565 (t0) cc_final: 0.8120 (m-40) REVERT: D 24 ARG cc_start: 0.8432 (ptt180) cc_final: 0.8229 (ptt180) REVERT: D 29 LYS cc_start: 0.8591 (tttp) cc_final: 0.8352 (tttm) REVERT: D 37 GLN cc_start: 0.8197 (mm110) cc_final: 0.7917 (mm110) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.3309 time to fit residues: 126.9115 Evaluate side-chains 200 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 232 ASN A 258 GLN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 609 GLN B 614 ASN E 105 HIS E 145 ASN F 90 GLN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 GLN C 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19865 Z= 0.155 Angle : 0.535 10.705 26888 Z= 0.281 Chirality : 0.042 0.185 2949 Planarity : 0.004 0.045 3440 Dihedral : 7.663 139.344 2663 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 1.24 % Allowed : 8.88 % Favored : 89.88 % 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: -1.23 (0.17), residues: 2391 helix: -0.25 (0.16), residues: 1084 sheet: 0.35 (0.36), residues: 212 loop : -1.61 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 480 HIS 0.005 0.001 HIS F 105 PHE 0.018 0.001 PHE A 19 TYR 0.018 0.001 TYR A 785 ARG 0.007 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7034 (tm-30) REVERT: A 464 GLU cc_start: 0.8003 (tt0) cc_final: 0.7788 (tt0) REVERT: B 574 MET cc_start: 0.8123 (mmm) cc_final: 0.7842 (mmm) REVERT: E 119 MET cc_start: 0.7464 (ttm) cc_final: 0.7234 (ttm) REVERT: E 146 ASP cc_start: 0.7297 (t0) cc_final: 0.7019 (t70) REVERT: E 210 CYS cc_start: 0.7204 (m) cc_final: 0.6770 (p) REVERT: F 308 MET cc_start: 0.7987 (tmm) cc_final: 0.7719 (tmm) REVERT: C 74 ASN cc_start: 0.8542 (t0) cc_final: 0.8112 (m-40) outliers start: 26 outliers final: 12 residues processed: 235 average time/residue: 0.3203 time to fit residues: 115.1539 Evaluate side-chains 205 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 145 ASN F 97 GLN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19865 Z= 0.249 Angle : 0.556 9.366 26888 Z= 0.292 Chirality : 0.043 0.150 2949 Planarity : 0.004 0.046 3440 Dihedral : 7.562 136.595 2663 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.91 % Allowed : 10.07 % Favored : 88.02 % 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 (0.17), residues: 2391 helix: -0.13 (0.16), residues: 1093 sheet: 0.41 (0.35), residues: 218 loop : -1.62 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 480 HIS 0.004 0.001 HIS B 561 PHE 0.019 0.001 PHE A 19 TYR 0.018 0.001 TYR B 273 ARG 0.007 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7182 (tm-30) REVERT: A 464 GLU cc_start: 0.8069 (tt0) cc_final: 0.7752 (tt0) REVERT: A 571 MET cc_start: 0.8519 (tpp) cc_final: 0.8247 (tpp) REVERT: B 574 MET cc_start: 0.8278 (mmm) cc_final: 0.8002 (mmm) REVERT: E 146 ASP cc_start: 0.7387 (t0) cc_final: 0.7106 (t70) REVERT: E 210 CYS cc_start: 0.7186 (m) cc_final: 0.6766 (p) REVERT: F 106 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7594 (ppp) REVERT: F 119 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5518 (mmt) REVERT: F 308 MET cc_start: 0.7935 (tmm) cc_final: 0.7674 (tmm) REVERT: D 24 ARG cc_start: 0.8359 (ptt180) cc_final: 0.8056 (ttp-170) outliers start: 40 outliers final: 25 residues processed: 228 average time/residue: 0.3129 time to fit residues: 110.2837 Evaluate side-chains 221 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 53 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 230 optimal weight: 0.0370 chunk 113 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 61 optimal weight: 0.0370 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 GLN ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 145 ASN ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19865 Z= 0.166 Angle : 0.513 8.532 26888 Z= 0.267 Chirality : 0.041 0.149 2949 Planarity : 0.004 0.047 3440 Dihedral : 7.316 134.451 2663 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.86 % Allowed : 11.41 % Favored : 86.73 % 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: -0.91 (0.17), residues: 2391 helix: 0.11 (0.16), residues: 1087 sheet: 0.45 (0.36), residues: 216 loop : -1.54 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 480 HIS 0.003 0.001 HIS E 105 PHE 0.020 0.001 PHE A 19 TYR 0.015 0.001 TYR A 275 ARG 0.007 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 209 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8202 (m-30) cc_final: 0.7987 (p0) REVERT: A 187 ASP cc_start: 0.8126 (m-30) cc_final: 0.7921 (m-30) REVERT: A 444 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 464 GLU cc_start: 0.8053 (tt0) cc_final: 0.7707 (tt0) REVERT: A 571 MET cc_start: 0.8550 (tpp) cc_final: 0.8314 (tpp) REVERT: B 574 MET cc_start: 0.8217 (mmm) cc_final: 0.7892 (mmm) REVERT: E 135 CYS cc_start: 0.7248 (m) cc_final: 0.6812 (t) REVERT: E 146 ASP cc_start: 0.7312 (t0) cc_final: 0.7012 (t70) REVERT: E 210 CYS cc_start: 0.7150 (m) cc_final: 0.6766 (p) REVERT: F 106 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7487 (ppp) REVERT: F 119 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5502 (mmt) REVERT: F 308 MET cc_start: 0.7996 (tmm) cc_final: 0.7754 (tmm) REVERT: C 74 ASN cc_start: 0.8526 (t0) cc_final: 0.8094 (m-40) REVERT: C 77 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7119 (tm-30) outliers start: 39 outliers final: 24 residues processed: 237 average time/residue: 0.3072 time to fit residues: 113.2322 Evaluate side-chains 229 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19865 Z= 0.215 Angle : 0.524 8.607 26888 Z= 0.274 Chirality : 0.042 0.147 2949 Planarity : 0.004 0.047 3440 Dihedral : 7.224 132.772 2663 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.10 % Allowed : 11.74 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2391 helix: 0.16 (0.16), residues: 1086 sheet: 0.41 (0.35), residues: 218 loop : -1.49 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 480 HIS 0.003 0.001 HIS B 561 PHE 0.010 0.001 PHE B 215 TYR 0.017 0.001 TYR A 275 ARG 0.007 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 208 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7199 (tm-30) REVERT: A 571 MET cc_start: 0.8556 (tpp) cc_final: 0.8318 (tpp) REVERT: B 467 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8123 (pp) REVERT: B 701 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9182 (mm) REVERT: E 210 CYS cc_start: 0.7213 (m) cc_final: 0.6825 (p) REVERT: F 106 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7560 (ppp) REVERT: F 119 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.5564 (mmt) REVERT: F 308 MET cc_start: 0.7931 (tmm) cc_final: 0.7683 (tmm) REVERT: C 77 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7047 (tm-30) outliers start: 44 outliers final: 30 residues processed: 242 average time/residue: 0.3111 time to fit residues: 116.6471 Evaluate side-chains 234 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 135 optimal weight: 0.0870 chunk 56 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19865 Z= 0.147 Angle : 0.502 8.274 26888 Z= 0.259 Chirality : 0.040 0.145 2949 Planarity : 0.004 0.046 3440 Dihedral : 6.997 130.328 2663 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.05 % Allowed : 12.22 % Favored : 85.73 % 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: -0.64 (0.17), residues: 2391 helix: 0.32 (0.17), residues: 1089 sheet: 0.49 (0.36), residues: 216 loop : -1.38 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 480 HIS 0.003 0.000 HIS A 226 PHE 0.009 0.001 PHE B 215 TYR 0.017 0.001 TYR F 142 ARG 0.007 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 212 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 571 MET cc_start: 0.8555 (tpp) cc_final: 0.8353 (tpp) REVERT: A 820 MET cc_start: 0.7863 (tmm) cc_final: 0.7601 (tmm) REVERT: B 574 MET cc_start: 0.8128 (mmm) cc_final: 0.7646 (mmm) REVERT: E 210 CYS cc_start: 0.7051 (m) cc_final: 0.6706 (p) REVERT: F 106 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7531 (ppp) REVERT: F 119 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5579 (mmt) REVERT: F 308 MET cc_start: 0.7993 (tmm) cc_final: 0.7731 (tmm) REVERT: C 15 ARG cc_start: 0.8624 (mmt90) cc_final: 0.8381 (mmt90) REVERT: C 77 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: D 24 ARG cc_start: 0.8236 (ttp-170) cc_final: 0.8030 (ttt-90) outliers start: 43 outliers final: 32 residues processed: 246 average time/residue: 0.3166 time to fit residues: 120.8388 Evaluate side-chains 235 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 44 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 131 optimal weight: 0.0980 chunk 168 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19865 Z= 0.199 Angle : 0.528 13.131 26888 Z= 0.270 Chirality : 0.042 0.147 2949 Planarity : 0.004 0.046 3440 Dihedral : 6.965 129.819 2663 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.34 % Allowed : 12.55 % Favored : 85.11 % 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: -0.60 (0.17), residues: 2391 helix: 0.37 (0.17), residues: 1083 sheet: 0.43 (0.35), residues: 218 loop : -1.34 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 480 HIS 0.003 0.001 HIS B 561 PHE 0.009 0.001 PHE B 215 TYR 0.016 0.001 TYR A 275 ARG 0.006 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 201 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7212 (tm-30) REVERT: A 571 MET cc_start: 0.8570 (tpp) cc_final: 0.8352 (tpp) REVERT: A 820 MET cc_start: 0.7940 (tmm) cc_final: 0.7690 (tmm) REVERT: B 127 ASP cc_start: 0.8321 (m-30) cc_final: 0.8100 (m-30) REVERT: B 574 MET cc_start: 0.8152 (mmm) cc_final: 0.7702 (mmm) REVERT: E 121 ASP cc_start: 0.8174 (t70) cc_final: 0.7785 (m-30) REVERT: E 210 CYS cc_start: 0.7133 (m) cc_final: 0.6817 (p) REVERT: F 106 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7482 (ppp) REVERT: F 119 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.5680 (mmt) REVERT: F 302 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.6971 (mt0) REVERT: F 308 MET cc_start: 0.7940 (tmm) cc_final: 0.7692 (tmm) REVERT: C 15 ARG cc_start: 0.8607 (mmt90) cc_final: 0.8374 (mmt90) REVERT: C 77 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: D 24 ARG cc_start: 0.8264 (ttp-170) cc_final: 0.8057 (ttt-90) outliers start: 49 outliers final: 39 residues processed: 237 average time/residue: 0.3168 time to fit residues: 116.4270 Evaluate side-chains 240 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 44 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19865 Z= 0.185 Angle : 0.522 11.487 26888 Z= 0.267 Chirality : 0.041 0.146 2949 Planarity : 0.004 0.046 3440 Dihedral : 6.853 129.090 2663 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.34 % Allowed : 12.60 % Favored : 85.06 % 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: -0.54 (0.17), residues: 2391 helix: 0.43 (0.17), residues: 1087 sheet: 0.46 (0.36), residues: 218 loop : -1.33 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 480 HIS 0.003 0.001 HIS B 561 PHE 0.008 0.001 PHE B 215 TYR 0.016 0.001 TYR B 97 ARG 0.006 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 195 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 820 MET cc_start: 0.8012 (tmm) cc_final: 0.7777 (tmm) REVERT: B 127 ASP cc_start: 0.8367 (m-30) cc_final: 0.8148 (m-30) REVERT: B 574 MET cc_start: 0.8174 (mmm) cc_final: 0.7717 (mmm) REVERT: E 121 ASP cc_start: 0.8161 (t70) cc_final: 0.7848 (m-30) REVERT: E 210 CYS cc_start: 0.7085 (m) cc_final: 0.6766 (p) REVERT: E 243 MET cc_start: 0.8617 (mtp) cc_final: 0.8385 (mtp) REVERT: F 119 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5664 (mmt) REVERT: F 302 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.6993 (mt0) REVERT: F 308 MET cc_start: 0.7947 (tmm) cc_final: 0.7699 (tmm) REVERT: C 15 ARG cc_start: 0.8646 (mmt90) cc_final: 0.8423 (mmt90) REVERT: C 77 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6900 (tm-30) outliers start: 49 outliers final: 39 residues processed: 231 average time/residue: 0.3131 time to fit residues: 112.7543 Evaluate side-chains 236 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 53 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 6.9990 chunk 219 optimal weight: 20.0000 chunk 200 optimal weight: 0.8980 chunk 213 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19865 Z= 0.192 Angle : 0.532 11.369 26888 Z= 0.272 Chirality : 0.041 0.146 2949 Planarity : 0.004 0.046 3440 Dihedral : 6.812 129.213 2663 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.24 % Allowed : 12.84 % Favored : 84.92 % 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: -0.52 (0.17), residues: 2391 helix: 0.46 (0.17), residues: 1085 sheet: 0.43 (0.35), residues: 218 loop : -1.33 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 480 HIS 0.003 0.001 HIS B 561 PHE 0.015 0.001 PHE F 65 TYR 0.016 0.001 TYR B 97 ARG 0.006 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 196 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8068 (ttm) cc_final: 0.7720 (mtp) REVERT: A 444 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 820 MET cc_start: 0.8096 (tmm) cc_final: 0.7873 (tmm) REVERT: B 127 ASP cc_start: 0.8348 (m-30) cc_final: 0.8129 (m-30) REVERT: B 574 MET cc_start: 0.8187 (mmm) cc_final: 0.7732 (mmm) REVERT: E 121 ASP cc_start: 0.8140 (t70) cc_final: 0.7867 (m-30) REVERT: E 210 CYS cc_start: 0.7071 (m) cc_final: 0.6741 (p) REVERT: F 302 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.6992 (mt0) REVERT: F 308 MET cc_start: 0.7946 (tmm) cc_final: 0.7697 (tmm) REVERT: C 15 ARG cc_start: 0.8645 (mmt90) cc_final: 0.8431 (mmt90) REVERT: C 77 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6886 (tm-30) outliers start: 47 outliers final: 40 residues processed: 232 average time/residue: 0.2948 time to fit residues: 106.3913 Evaluate side-chains 236 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 53 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 237 optimal weight: 20.0000 chunk 218 optimal weight: 0.7980 chunk 188 optimal weight: 8.9990 chunk 19 optimal weight: 0.0770 chunk 145 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 overall best weight: 1.3140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19865 Z= 0.177 Angle : 0.534 11.094 26888 Z= 0.272 Chirality : 0.041 0.146 2949 Planarity : 0.004 0.045 3440 Dihedral : 6.733 128.923 2663 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.96 % Allowed : 13.37 % Favored : 84.68 % 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: -0.47 (0.17), residues: 2391 helix: 0.50 (0.17), residues: 1084 sheet: 0.44 (0.36), residues: 218 loop : -1.29 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 480 HIS 0.003 0.001 HIS B 561 PHE 0.014 0.001 PHE F 65 TYR 0.015 0.001 TYR B 97 ARG 0.006 0.000 ARG B 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 197 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7924 (tp30) REVERT: A 138 MET cc_start: 0.8094 (ttm) cc_final: 0.7803 (mtp) REVERT: A 444 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 820 MET cc_start: 0.8110 (tmm) cc_final: 0.7892 (tmm) REVERT: B 127 ASP cc_start: 0.8357 (m-30) cc_final: 0.8133 (m-30) REVERT: B 574 MET cc_start: 0.8179 (mmm) cc_final: 0.7838 (mmm) REVERT: E 121 ASP cc_start: 0.8085 (t70) cc_final: 0.7866 (m-30) REVERT: E 210 CYS cc_start: 0.7056 (m) cc_final: 0.6760 (p) REVERT: E 243 MET cc_start: 0.8631 (mtp) cc_final: 0.8398 (mtp) REVERT: F 119 MET cc_start: 0.6932 (mpp) cc_final: 0.6554 (mpp) REVERT: F 302 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7022 (mt0) REVERT: F 308 MET cc_start: 0.7939 (tmm) cc_final: 0.7697 (tmm) REVERT: C 15 ARG cc_start: 0.8652 (mmt90) cc_final: 0.8450 (mmt90) REVERT: C 77 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6881 (tm-30) outliers start: 41 outliers final: 38 residues processed: 229 average time/residue: 0.3266 time to fit residues: 116.4102 Evaluate side-chains 236 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 196 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 268 ASP Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN E 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.101169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.067528 restraints weight = 42395.554| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.01 r_work: 0.2813 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19865 Z= 0.291 Angle : 0.591 11.750 26888 Z= 0.305 Chirality : 0.044 0.156 2949 Planarity : 0.004 0.048 3440 Dihedral : 6.977 129.089 2663 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.05 % Allowed : 13.27 % Favored : 84.68 % 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: -0.69 (0.17), residues: 2391 helix: 0.33 (0.17), residues: 1083 sheet: 0.31 (0.35), residues: 218 loop : -1.41 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 480 HIS 0.004 0.001 HIS B 561 PHE 0.015 0.001 PHE F 65 TYR 0.020 0.001 TYR A 275 ARG 0.005 0.000 ARG B 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4071.92 seconds wall clock time: 74 minutes 34.58 seconds (4474.58 seconds total)