Starting phenix.real_space_refine on Wed Aug 7 20:37:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ari_43783/08_2024/9ari_43783.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ari_43783/08_2024/9ari_43783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ari_43783/08_2024/9ari_43783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ari_43783/08_2024/9ari_43783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ari_43783/08_2024/9ari_43783.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ari_43783/08_2024/9ari_43783.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 13348 2.51 5 N 3454 2.21 5 O 3866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20756 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 5296 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 36, 'TRANS': 764} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1059 Unresolved non-hydrogen angles: 1295 Unresolved non-hydrogen dihedrals: 890 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 24, 'TYR:plan': 9, 'ASN:plan1': 24, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 5, 'GLU:plan': 41, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 745 Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5072 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 28, 'TRANS': 758} Chain breaks: 2 Unresolved non-hydrogen bonds: 1194 Unresolved non-hydrogen angles: 1481 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 36, 'TYR:plan': 17, 'ASN:plan1': 18, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 16, 'GLU:plan': 46, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 809 Chain: "C" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 5296 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 36, 'TRANS': 764} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1059 Unresolved non-hydrogen angles: 1295 Unresolved non-hydrogen dihedrals: 890 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 24, 'TYR:plan': 9, 'ASN:plan1': 24, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 5, 'GLU:plan': 41, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 745 Chain: "D" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5072 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 28, 'TRANS': 758} Chain breaks: 2 Unresolved non-hydrogen bonds: 1194 Unresolved non-hydrogen angles: 1481 Unresolved non-hydrogen dihedrals: 1034 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 36, 'TYR:plan': 17, 'ASN:plan1': 18, 'TRP:plan': 4, 'HIS:plan': 8, 'PHE:plan': 16, 'GLU:plan': 46, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 809 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 11.45, per 1000 atoms: 0.55 Number of scatterers: 20756 At special positions: 0 Unit cell: (146.59, 129.47, 180.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3866 8.00 N 3454 7.00 C 13348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.75 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=1.96 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.02 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=1.67 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.75 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.45 Conformation dependent library (CDL) restraints added in 4.3 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5936 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 34 sheets defined 42.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 103 through 113 removed outlier: 4.269A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.793A pdb=" N TYR A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 removed outlier: 4.071A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.720A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 Processing helix chain 'A' and resid 272 through 275 removed outlier: 3.567A pdb=" N ILE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 297 through 317 Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.906A pdb=" N LEU A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.640A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 605 removed outlier: 3.711A pdb=" N SER A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 634 Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.715A pdb=" N MET A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 removed outlier: 3.572A pdb=" N ARG A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.798A pdb=" N GLN A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.571A pdb=" N THR A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 744 Processing helix chain 'A' and resid 754 through 762 Processing helix chain 'A' and resid 787 through 803 removed outlier: 4.038A pdb=" N GLN A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 834 through 862 removed outlier: 4.145A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 862 " --> pdb=" O TYR A 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.290A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.546A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 209 through 222 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.107A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 523 removed outlier: 4.312A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 580 removed outlier: 3.621A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.826A pdb=" N GLN B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 709 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 772 through 786 Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.675A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 794 " --> pdb=" O GLU B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 844 removed outlier: 3.513A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.738A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 113 removed outlier: 4.268A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.793A pdb=" N TYR C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 removed outlier: 4.071A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.720A pdb=" N GLU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 260 Processing helix chain 'C' and resid 272 through 275 removed outlier: 3.566A pdb=" N ILE C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 275' Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 297 through 317 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.906A pdb=" N LEU C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 521 through 529 removed outlier: 3.640A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 605 removed outlier: 3.710A pdb=" N SER C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 634 Processing helix chain 'C' and resid 647 through 676 removed outlier: 3.715A pdb=" N MET C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 removed outlier: 3.572A pdb=" N ARG C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.799A pdb=" N GLN C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 729 removed outlier: 3.571A pdb=" N THR C 722 " --> pdb=" O VAL C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 744 Processing helix chain 'C' and resid 754 through 762 Processing helix chain 'C' and resid 787 through 803 removed outlier: 4.037A pdb=" N GLN C 791 " --> pdb=" O SER C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 834 through 862 removed outlier: 4.145A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 862 " --> pdb=" O TYR C 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 removed outlier: 4.290A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.545A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 209 through 222 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 324 through 330 Processing helix chain 'D' and resid 334 through 340 removed outlier: 4.108A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 472 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 523 removed outlier: 4.312A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 580 removed outlier: 3.621A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.825A pdb=" N GLN D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 709 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 772 through 786 Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.675A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 794 " --> pdb=" O GLU D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 844 removed outlier: 3.513A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.423A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 138 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 removed outlier: 3.634A pdb=" N LEU A 242 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 292 removed outlier: 6.925A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 394 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 389 " --> pdb=" O HIS A 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 361 removed outlier: 3.778A pdb=" N GLU A 360 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 421 through 422 removed outlier: 3.755A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 783 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A 549 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 433 Processing sheet with id=AA8, first strand: chain 'A' and resid 702 through 703 removed outlier: 7.022A pdb=" N ALA A 703 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ASP A 753 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 750 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 562 " --> pdb=" O PHE A 750 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 560 " --> pdb=" O TRP A 752 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 69 removed outlier: 7.328A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 69 removed outlier: 7.461A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 144 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 205 removed outlier: 8.346A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU B 205 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR B 173 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 278 through 281 removed outlier: 6.854A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 376 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 408 Processing sheet with id=AB6, first strand: chain 'B' and resid 434 through 438 removed outlier: 3.736A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 455 " --> pdb=" O CYS B 436 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 438 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 453 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 508 through 509 removed outlier: 3.603A pdb=" N ALA B 509 " --> pdb=" O ALA B 765 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 730 through 732 removed outlier: 3.624A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 26 through 33 Processing sheet with id=AC1, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.423A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 138 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.633A pdb=" N LEU C 242 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 290 through 292 removed outlier: 6.925A pdb=" N ASN C 376 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN C 384 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 394 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN C 389 " --> pdb=" O HIS C 392 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 360 through 361 removed outlier: 3.779A pdb=" N GLU C 360 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 421 through 422 removed outlier: 3.755A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 783 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C 549 " --> pdb=" O MET C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 431 through 433 Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 703 removed outlier: 7.022A pdb=" N ALA C 703 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ASP C 753 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE C 750 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 562 " --> pdb=" O PHE C 750 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP C 752 " --> pdb=" O THR C 560 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 560 " --> pdb=" O TRP C 752 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 66 through 69 removed outlier: 7.328A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 66 through 69 removed outlier: 7.461A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE D 40 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE D 144 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 198 through 205 removed outlier: 8.346A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU D 205 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR D 173 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 278 through 281 removed outlier: 6.855A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 376 " --> pdb=" O ILE D 364 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 379 through 380 Processing sheet with id=AD4, first strand: chain 'D' and resid 405 through 408 Processing sheet with id=AD5, first strand: chain 'D' and resid 434 through 438 removed outlier: 3.736A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D 455 " --> pdb=" O CYS D 436 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 438 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE D 453 " --> pdb=" O LYS D 438 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 508 through 509 removed outlier: 3.603A pdb=" N ALA D 509 " --> pdb=" O ALA D 765 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 730 through 732 removed outlier: 3.624A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3048 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: 7.18 Time building geometry restraints manager: 8.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 3398 1.25 - 1.39: 4826 1.39 - 1.54: 12337 1.54 - 1.68: 459 1.68 - 1.82: 136 Bond restraints: 21156 Sorted by residual: bond pdb=" C THR C 669 " pdb=" O THR C 669 " ideal model delta sigma weight residual 1.236 1.110 0.126 1.26e-02 6.30e+03 1.00e+02 bond pdb=" C THR A 669 " pdb=" O THR A 669 " ideal model delta sigma weight residual 1.236 1.111 0.126 1.26e-02 6.30e+03 9.96e+01 bond pdb=" C ASN A 671 " pdb=" O ASN A 671 " ideal model delta sigma weight residual 1.236 1.124 0.113 1.15e-02 7.56e+03 9.62e+01 bond pdb=" C ASN C 671 " pdb=" O ASN C 671 " ideal model delta sigma weight residual 1.236 1.124 0.113 1.15e-02 7.56e+03 9.60e+01 bond pdb=" C ALA C 670 " pdb=" O ALA C 670 " ideal model delta sigma weight residual 1.236 1.132 0.105 1.15e-02 7.56e+03 8.27e+01 ... (remaining 21151 not shown) Histogram of bond angle deviations from ideal: 87.27 - 96.68: 10 96.68 - 106.10: 630 106.10 - 115.51: 13338 115.51 - 124.92: 14789 124.92 - 134.33: 429 Bond angle restraints: 29196 Sorted by residual: angle pdb=" C PHE A 479 " pdb=" CA PHE A 479 " pdb=" CB PHE A 479 " ideal model delta sigma weight residual 110.88 87.27 23.61 1.57e+00 4.06e-01 2.26e+02 angle pdb=" C PHE C 479 " pdb=" CA PHE C 479 " pdb=" CB PHE C 479 " ideal model delta sigma weight residual 110.88 87.29 23.59 1.57e+00 4.06e-01 2.26e+02 angle pdb=" C LEU C 635 " pdb=" N LEU C 636 " pdb=" CA LEU C 636 " ideal model delta sigma weight residual 122.95 106.94 16.01 1.66e+00 3.63e-01 9.30e+01 angle pdb=" N ILE C 797 " pdb=" CA ILE C 797 " pdb=" CB ILE C 797 " ideal model delta sigma weight residual 110.54 123.10 -12.56 1.36e+00 5.41e-01 8.53e+01 angle pdb=" N ILE A 797 " pdb=" CA ILE A 797 " pdb=" CB ILE A 797 " ideal model delta sigma weight residual 110.54 123.09 -12.55 1.36e+00 5.41e-01 8.52e+01 ... (remaining 29191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.34: 11482 14.34 - 28.68: 531 28.68 - 43.02: 205 43.02 - 57.35: 52 57.35 - 71.69: 8 Dihedral angle restraints: 12278 sinusoidal: 3120 harmonic: 9158 Sorted by residual: dihedral pdb=" C PHE A 479 " pdb=" N PHE A 479 " pdb=" CA PHE A 479 " pdb=" CB PHE A 479 " ideal model delta harmonic sigma weight residual -122.60 -93.55 -29.05 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" C PHE C 479 " pdb=" N PHE C 479 " pdb=" CA PHE C 479 " pdb=" CB PHE C 479 " ideal model delta harmonic sigma weight residual -122.60 -93.59 -29.01 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" C ASN B 615 " pdb=" N ASN B 615 " pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " ideal model delta harmonic sigma weight residual -122.60 -150.52 27.92 0 2.50e+00 1.60e-01 1.25e+02 ... (remaining 12275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 3707 0.225 - 0.450: 59 0.450 - 0.675: 10 0.675 - 0.900: 4 0.900 - 1.125: 2 Chirality restraints: 3782 Sorted by residual: chirality pdb=" CA ASN B 615 " pdb=" N ASN B 615 " pdb=" C ASN B 615 " pdb=" CB ASN B 615 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.13 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA ASN D 615 " pdb=" N ASN D 615 " pdb=" C ASN D 615 " pdb=" CB ASN D 615 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA PHE C 675 " pdb=" N PHE C 675 " pdb=" C PHE C 675 " pdb=" CB PHE C 675 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 3779 not shown) Planarity restraints: 3706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 830 " 0.029 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C THR C 830 " -0.105 2.00e-02 2.50e+03 pdb=" O THR C 830 " 0.040 2.00e-02 2.50e+03 pdb=" N CYS C 831 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 830 " 0.029 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C THR A 830 " -0.104 2.00e-02 2.50e+03 pdb=" O THR A 830 " 0.040 2.00e-02 2.50e+03 pdb=" N CYS A 831 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 616 " -0.027 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C ASN B 616 " 0.100 2.00e-02 2.50e+03 pdb=" O ASN B 616 " -0.039 2.00e-02 2.50e+03 pdb=" N SER B 617 " -0.034 2.00e-02 2.50e+03 ... (remaining 3703 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 67 2.43 - 3.05: 14056 3.05 - 3.67: 30282 3.67 - 4.28: 39833 4.28 - 4.90: 65322 Nonbonded interactions: 149560 Sorted by model distance: nonbonded pdb=" O LEU D 513 " pdb=" CG2 THR D 514 " model vdw 1.816 3.460 nonbonded pdb=" O LEU B 513 " pdb=" CG2 THR B 514 " model vdw 1.816 3.460 nonbonded pdb=" O GLY A 459 " pdb=" N ASN A 461 " model vdw 1.891 3.120 nonbonded pdb=" O GLY C 459 " pdb=" N ASN C 461 " model vdw 1.891 3.120 nonbonded pdb=" OG SER A 638 " pdb=" N GLY A 639 " model vdw 1.961 3.120 ... (remaining 149555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 54.400 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 21156 Z= 0.464 Angle : 1.123 23.607 29196 Z= 0.741 Chirality : 0.075 1.125 3782 Planarity : 0.007 0.063 3706 Dihedral : 10.705 71.692 6288 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.86 % Favored : 92.88 % Rotamer: Outliers : 9.33 % Allowed : 8.80 % Favored : 81.87 % Cbeta Deviations : 1.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.13), residues: 3148 helix: -0.70 (0.13), residues: 1350 sheet: -3.15 (0.21), residues: 414 loop : -3.47 (0.14), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 632 HIS 0.006 0.001 HIS A 801 PHE 0.039 0.002 PHE A 429 TYR 0.022 0.001 TYR D 843 ARG 0.007 0.001 ARG C 651 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 430 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7952 (pp30) REVERT: A 597 MET cc_start: 0.8061 (ttt) cc_final: 0.7525 (ttm) REVERT: A 783 MET cc_start: 0.7913 (tpp) cc_final: 0.7591 (tpp) REVERT: A 801 HIS cc_start: 0.9323 (OUTLIER) cc_final: 0.8852 (t-90) REVERT: B 184 ASN cc_start: 0.8790 (m110) cc_final: 0.8587 (m-40) REVERT: B 232 CYS cc_start: 0.6404 (t) cc_final: 0.5849 (t) REVERT: B 467 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8231 (mptt) REVERT: B 480 LEU cc_start: 0.7577 (tp) cc_final: 0.7241 (tt) REVERT: B 782 GLN cc_start: 0.8326 (pp30) cc_final: 0.8054 (tm-30) REVERT: C 546 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7882 (pp30) REVERT: C 801 HIS cc_start: 0.9303 (OUTLIER) cc_final: 0.8455 (t-90) REVERT: D 467 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8002 (mmtm) REVERT: D 782 GLN cc_start: 0.8435 (pp30) cc_final: 0.8090 (tm-30) REVERT: D 795 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9247 (tp) outliers start: 159 outliers final: 68 residues processed: 568 average time/residue: 0.2575 time to fit residues: 241.9316 Evaluate side-chains 365 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 294 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 834 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 20.0000 chunk 239 optimal weight: 50.0000 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 161 optimal weight: 20.0000 chunk 127 optimal weight: 0.7980 chunk 247 optimal weight: 50.0000 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 286 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 498 HIS A 577 GLN A 792 GLN B 357 GLN B 615 ASN B 710 ASN B 775 GLN C 159 ASN C 498 HIS C 577 GLN C 748 HIS C 792 GLN D 357 GLN D 615 ASN D 710 ASN D 775 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21156 Z= 0.256 Angle : 0.628 7.713 29196 Z= 0.331 Chirality : 0.044 0.247 3782 Planarity : 0.004 0.054 3706 Dihedral : 7.197 74.887 3365 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.59 % Favored : 92.34 % Rotamer: Outliers : 7.45 % Allowed : 15.90 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.14), residues: 3148 helix: 0.32 (0.14), residues: 1344 sheet: -2.70 (0.22), residues: 418 loop : -2.95 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 559 HIS 0.005 0.001 HIS C 592 PHE 0.035 0.002 PHE A 579 TYR 0.018 0.001 TYR C 599 ARG 0.009 0.001 ARG C 743 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 311 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 MET cc_start: 0.8552 (ttt) cc_final: 0.8328 (ttm) REVERT: A 775 PHE cc_start: 0.8040 (t80) cc_final: 0.7830 (t80) REVERT: A 801 HIS cc_start: 0.9039 (OUTLIER) cc_final: 0.8378 (t-90) REVERT: B 186 ILE cc_start: 0.9252 (pt) cc_final: 0.8972 (tp) REVERT: B 232 CYS cc_start: 0.6560 (t) cc_final: 0.5877 (t) REVERT: B 240 ILE cc_start: 0.8243 (tp) cc_final: 0.7987 (mt) REVERT: B 357 GLN cc_start: 0.7099 (mt0) cc_final: 0.6318 (pp30) REVERT: B 429 CYS cc_start: 0.4628 (OUTLIER) cc_final: 0.4271 (t) REVERT: B 467 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8236 (mptt) REVERT: B 476 TYR cc_start: 0.8056 (p90) cc_final: 0.7592 (p90) REVERT: C 767 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9186 (pp) REVERT: C 801 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.8281 (t-90) REVERT: D 433 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7998 (t) REVERT: D 467 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8236 (mptt) REVERT: D 782 GLN cc_start: 0.8452 (pp30) cc_final: 0.8240 (tm-30) REVERT: D 795 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9324 (tp) outliers start: 127 outliers final: 70 residues processed: 415 average time/residue: 0.2566 time to fit residues: 179.4138 Evaluate side-chains 352 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 276 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 30.0000 chunk 89 optimal weight: 20.0000 chunk 238 optimal weight: 50.0000 chunk 195 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 310 optimal weight: 0.6980 chunk 256 optimal weight: 7.9990 chunk 285 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN C 748 HIS D 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21156 Z= 0.256 Angle : 0.609 7.972 29196 Z= 0.317 Chirality : 0.044 0.230 3782 Planarity : 0.004 0.048 3706 Dihedral : 6.390 74.235 3314 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 7.75 % Allowed : 16.78 % Favored : 75.47 % 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: -1.75 (0.15), residues: 3148 helix: 0.71 (0.14), residues: 1336 sheet: -2.44 (0.23), residues: 424 loop : -2.69 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.004 0.001 HIS B 486 PHE 0.027 0.002 PHE A 579 TYR 0.011 0.001 TYR A 599 ARG 0.004 0.000 ARG C 743 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 284 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8633 (pt) cc_final: 0.8002 (tp) REVERT: A 797 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7595 (pt) REVERT: A 801 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8345 (t-90) REVERT: B 186 ILE cc_start: 0.9288 (pt) cc_final: 0.8938 (tp) REVERT: B 240 ILE cc_start: 0.8295 (tp) cc_final: 0.8038 (mt) REVERT: B 357 GLN cc_start: 0.7119 (mt0) cc_final: 0.6112 (pp30) REVERT: B 467 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8248 (mptt) REVERT: C 91 LEU cc_start: 0.8702 (pt) cc_final: 0.8039 (tp) REVERT: C 748 HIS cc_start: 0.8788 (OUTLIER) cc_final: 0.8485 (m170) REVERT: C 767 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9160 (pp) REVERT: C 797 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7721 (pt) REVERT: C 801 HIS cc_start: 0.8927 (OUTLIER) cc_final: 0.8234 (t-90) REVERT: D 357 GLN cc_start: 0.7592 (mt0) cc_final: 0.6935 (pp30) REVERT: D 433 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8025 (t) REVERT: D 795 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9248 (tt) outliers start: 132 outliers final: 92 residues processed: 389 average time/residue: 0.2499 time to fit residues: 162.4763 Evaluate side-chains 362 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 262 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 748 HIS Chi-restraints excluded: chain C residue 758 GLU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 305 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 273 optimal weight: 0.0170 chunk 82 optimal weight: 50.0000 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN C 748 HIS D 184 ASN D 703 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21156 Z= 0.224 Angle : 0.587 7.596 29196 Z= 0.304 Chirality : 0.043 0.194 3782 Planarity : 0.004 0.044 3706 Dihedral : 6.302 70.384 3312 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 8.69 % Allowed : 17.02 % Favored : 74.30 % 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: -1.49 (0.15), residues: 3148 helix: 0.90 (0.14), residues: 1354 sheet: -2.30 (0.23), residues: 428 loop : -2.56 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 197 HIS 0.017 0.001 HIS C 748 PHE 0.021 0.001 PHE A 579 TYR 0.010 0.001 TYR A 599 ARG 0.002 0.000 ARG C 743 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 273 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5137 (OUTLIER) cc_final: 0.4810 (mm) REVERT: A 91 LEU cc_start: 0.8654 (pt) cc_final: 0.8039 (tp) REVERT: A 797 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7927 (tt) REVERT: A 801 HIS cc_start: 0.8894 (OUTLIER) cc_final: 0.8249 (t-90) REVERT: B 186 ILE cc_start: 0.9249 (pt) cc_final: 0.8931 (tp) REVERT: B 240 ILE cc_start: 0.8309 (tp) cc_final: 0.8056 (mt) REVERT: B 357 GLN cc_start: 0.7102 (mt0) cc_final: 0.6184 (pp30) REVERT: B 433 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7976 (t) REVERT: B 467 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8211 (mptt) REVERT: B 476 TYR cc_start: 0.8106 (p90) cc_final: 0.7648 (p90) REVERT: C 26 ILE cc_start: 0.4962 (OUTLIER) cc_final: 0.4682 (mm) REVERT: C 91 LEU cc_start: 0.8735 (pt) cc_final: 0.8167 (tp) REVERT: C 164 ILE cc_start: 0.8760 (mt) cc_final: 0.8540 (mp) REVERT: C 767 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9131 (pp) REVERT: C 783 MET cc_start: 0.7908 (tpp) cc_final: 0.7196 (tpp) REVERT: C 786 ASP cc_start: 0.7064 (p0) cc_final: 0.6857 (p0) REVERT: C 801 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8213 (t-90) REVERT: D 357 GLN cc_start: 0.7504 (mt0) cc_final: 0.7054 (pp30) REVERT: D 433 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7949 (t) REVERT: D 467 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8230 (mptt) REVERT: D 795 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9261 (tt) outliers start: 148 outliers final: 97 residues processed: 398 average time/residue: 0.2576 time to fit residues: 172.8663 Evaluate side-chains 366 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 260 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 227 optimal weight: 0.8980 chunk 126 optimal weight: 0.3980 chunk 260 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 0 optimal weight: 60.0000 chunk 155 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21156 Z= 0.168 Angle : 0.568 10.082 29196 Z= 0.287 Chirality : 0.042 0.165 3782 Planarity : 0.003 0.044 3706 Dihedral : 5.785 64.038 3304 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 7.86 % Allowed : 18.25 % Favored : 73.88 % 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: -1.14 (0.15), residues: 3148 helix: 1.20 (0.14), residues: 1338 sheet: -1.96 (0.24), residues: 408 loop : -2.42 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 197 HIS 0.003 0.001 HIS B 486 PHE 0.017 0.001 PHE A 579 TYR 0.009 0.001 TYR B 239 ARG 0.002 0.000 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 284 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5058 (OUTLIER) cc_final: 0.4767 (mm) REVERT: A 91 LEU cc_start: 0.8692 (pt) cc_final: 0.8110 (tp) REVERT: A 534 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 767 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9160 (pp) REVERT: A 775 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: A 797 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7463 (pt) REVERT: B 186 ILE cc_start: 0.9278 (pt) cc_final: 0.8924 (tp) REVERT: B 240 ILE cc_start: 0.8301 (tp) cc_final: 0.8054 (mt) REVERT: B 357 GLN cc_start: 0.7037 (mt0) cc_final: 0.6210 (pp30) REVERT: B 467 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8235 (mptt) REVERT: C 26 ILE cc_start: 0.4879 (OUTLIER) cc_final: 0.4639 (mm) REVERT: C 91 LEU cc_start: 0.8683 (pt) cc_final: 0.8112 (tp) REVERT: C 767 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9099 (pp) REVERT: C 775 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7261 (m-80) REVERT: C 783 MET cc_start: 0.7693 (tpp) cc_final: 0.7388 (ttm) REVERT: C 806 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8733 (mpp) REVERT: D 357 GLN cc_start: 0.7240 (mt0) cc_final: 0.6661 (pp30) REVERT: D 433 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.8021 (t) REVERT: D 467 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8153 (mptt) REVERT: D 654 MET cc_start: 0.7940 (ttm) cc_final: 0.7393 (ttp) REVERT: D 795 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9272 (tt) outliers start: 134 outliers final: 85 residues processed: 394 average time/residue: 0.2439 time to fit residues: 161.4008 Evaluate side-chains 362 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 266 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 806 MET Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 305 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 141 optimal weight: 0.4980 chunk 25 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 160 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 HIS D 184 ASN D 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21156 Z= 0.170 Angle : 0.574 15.421 29196 Z= 0.287 Chirality : 0.042 0.183 3782 Planarity : 0.003 0.044 3706 Dihedral : 5.169 55.254 3286 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 7.10 % Allowed : 19.84 % Favored : 73.06 % 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: -0.98 (0.15), residues: 3148 helix: 1.33 (0.15), residues: 1330 sheet: -1.82 (0.25), residues: 408 loop : -2.33 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 796 HIS 0.003 0.001 HIS B 486 PHE 0.016 0.001 PHE C 579 TYR 0.010 0.001 TYR B 239 ARG 0.004 0.000 ARG C 716 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 273 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.4993 (OUTLIER) cc_final: 0.4731 (mm) REVERT: A 91 LEU cc_start: 0.8683 (pt) cc_final: 0.8050 (tp) REVERT: A 775 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: B 186 ILE cc_start: 0.9289 (pt) cc_final: 0.8951 (tp) REVERT: B 240 ILE cc_start: 0.8318 (tp) cc_final: 0.8075 (mt) REVERT: B 357 GLN cc_start: 0.7100 (mt0) cc_final: 0.6323 (pp30) REVERT: B 405 HIS cc_start: 0.7349 (t70) cc_final: 0.6975 (t70) REVERT: B 433 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7967 (t) REVERT: B 467 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8207 (mptt) REVERT: B 476 TYR cc_start: 0.8123 (p90) cc_final: 0.7663 (p90) REVERT: C 26 ILE cc_start: 0.4800 (OUTLIER) cc_final: 0.4584 (mm) REVERT: C 91 LEU cc_start: 0.8666 (pt) cc_final: 0.8176 (tt) REVERT: C 532 ASP cc_start: 0.8487 (t70) cc_final: 0.8264 (t0) REVERT: C 767 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9116 (pp) REVERT: C 775 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7189 (m-80) REVERT: C 783 MET cc_start: 0.7769 (tpp) cc_final: 0.7535 (ttm) REVERT: D 357 GLN cc_start: 0.6991 (mt0) cc_final: 0.6452 (pp30) REVERT: D 433 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.8026 (t) REVERT: D 467 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8219 (mptt) REVERT: D 795 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9237 (tt) outliers start: 121 outliers final: 91 residues processed: 375 average time/residue: 0.2466 time to fit residues: 155.9742 Evaluate side-chains 359 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 260 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 818 MET Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 0.1980 chunk 34 optimal weight: 0.0870 chunk 174 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 304 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN B 697 ASN B 703 HIS D 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21156 Z= 0.210 Angle : 0.585 12.658 29196 Z= 0.294 Chirality : 0.042 0.161 3782 Planarity : 0.003 0.043 3706 Dihedral : 5.123 55.389 3284 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 7.16 % Allowed : 20.19 % Favored : 72.65 % 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: -0.89 (0.15), residues: 3148 helix: 1.36 (0.15), residues: 1324 sheet: -1.70 (0.26), residues: 390 loop : -2.24 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.003 0.001 HIS A 801 PHE 0.019 0.001 PHE A 579 TYR 0.011 0.001 TYR B 239 ARG 0.004 0.000 ARG C 716 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 259 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.4871 (OUTLIER) cc_final: 0.4634 (mm) REVERT: A 91 LEU cc_start: 0.8700 (pt) cc_final: 0.8084 (tp) REVERT: A 775 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: A 776 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7237 (mmm-85) REVERT: B 184 ASN cc_start: 0.8464 (m110) cc_final: 0.8180 (p0) REVERT: B 186 ILE cc_start: 0.9285 (pt) cc_final: 0.8952 (tp) REVERT: B 240 ILE cc_start: 0.8344 (tp) cc_final: 0.8095 (mt) REVERT: B 357 GLN cc_start: 0.7144 (mt0) cc_final: 0.6361 (pp30) REVERT: B 405 HIS cc_start: 0.7393 (t70) cc_final: 0.7039 (t70) REVERT: B 433 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.8003 (t) REVERT: B 467 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8186 (mptt) REVERT: C 91 LEU cc_start: 0.8747 (pt) cc_final: 0.8163 (tp) REVERT: C 767 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9122 (pp) REVERT: C 775 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: C 783 MET cc_start: 0.7778 (tpp) cc_final: 0.7473 (ttm) REVERT: D 357 GLN cc_start: 0.6997 (mt0) cc_final: 0.6449 (pp30) REVERT: D 433 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.8031 (t) REVERT: D 467 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8178 (mptt) REVERT: D 795 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9255 (tt) outliers start: 122 outliers final: 96 residues processed: 362 average time/residue: 0.2530 time to fit residues: 154.0513 Evaluate side-chains 359 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 256 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 818 MET Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 30.0000 chunk 121 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 193 optimal weight: 0.0040 chunk 207 optimal weight: 0.0980 chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 30.0000 chunk 239 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 184 ASN D 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21156 Z= 0.223 Angle : 0.584 9.741 29196 Z= 0.296 Chirality : 0.043 0.156 3782 Planarity : 0.003 0.044 3706 Dihedral : 5.163 55.498 3284 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 7.22 % Allowed : 20.31 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3148 helix: 1.39 (0.15), residues: 1324 sheet: -1.70 (0.26), residues: 394 loop : -2.16 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 635 HIS 0.003 0.001 HIS A 801 PHE 0.018 0.001 PHE A 579 TYR 0.011 0.001 TYR B 239 ARG 0.004 0.000 ARG C 716 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 257 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.4994 (OUTLIER) cc_final: 0.4772 (mm) REVERT: A 91 LEU cc_start: 0.8717 (pt) cc_final: 0.8126 (tp) REVERT: A 776 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7353 (mmm-85) REVERT: A 783 MET cc_start: 0.7732 (tpp) cc_final: 0.7475 (ttm) REVERT: B 184 ASN cc_start: 0.8424 (m110) cc_final: 0.8132 (p0) REVERT: B 186 ILE cc_start: 0.9282 (pt) cc_final: 0.8951 (tp) REVERT: B 240 ILE cc_start: 0.8359 (tp) cc_final: 0.8110 (mt) REVERT: B 357 GLN cc_start: 0.7105 (mt0) cc_final: 0.6351 (pp30) REVERT: B 405 HIS cc_start: 0.7500 (t70) cc_final: 0.7119 (t70) REVERT: B 433 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7996 (t) REVERT: B 467 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8195 (mptt) REVERT: B 476 TYR cc_start: 0.8114 (p90) cc_final: 0.7660 (p90) REVERT: C 91 LEU cc_start: 0.8732 (pt) cc_final: 0.8153 (tp) REVERT: C 767 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9080 (pp) REVERT: C 775 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: C 783 MET cc_start: 0.7872 (tpp) cc_final: 0.7585 (ttm) REVERT: D 357 GLN cc_start: 0.7011 (mt0) cc_final: 0.6524 (pp30) REVERT: D 433 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8026 (t) REVERT: D 467 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8163 (mptt) REVERT: D 795 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9272 (tt) REVERT: B 901 GLU cc_start: 0.4867 (mm-30) cc_final: 0.4650 (mm-30) outliers start: 123 outliers final: 98 residues processed: 362 average time/residue: 0.2483 time to fit residues: 151.0448 Evaluate side-chains 351 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 247 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 818 MET Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 6.9990 chunk 266 optimal weight: 0.6980 chunk 283 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 222 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 268 optimal weight: 40.0000 chunk 282 optimal weight: 4.9990 chunk 186 optimal weight: 50.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 21156 Z= 0.406 Angle : 0.682 8.791 29196 Z= 0.355 Chirality : 0.045 0.204 3782 Planarity : 0.004 0.045 3706 Dihedral : 5.536 54.479 3283 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.02 % Favored : 90.91 % Rotamer: Outliers : 7.10 % Allowed : 20.72 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.07 (0.15), residues: 3148 helix: 1.11 (0.15), residues: 1320 sheet: -1.60 (0.26), residues: 392 loop : -2.29 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 559 HIS 0.006 0.001 HIS A 801 PHE 0.027 0.002 PHE A 579 TYR 0.015 0.002 TYR A 599 ARG 0.004 0.001 ARG D 774 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 253 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8755 (pt) cc_final: 0.8178 (tp) REVERT: A 523 MET cc_start: 0.8398 (mmt) cc_final: 0.8163 (mmt) REVERT: A 783 MET cc_start: 0.8021 (tpp) cc_final: 0.7368 (ttm) REVERT: B 186 ILE cc_start: 0.9281 (pt) cc_final: 0.8942 (tp) REVERT: B 240 ILE cc_start: 0.8440 (tp) cc_final: 0.8188 (mt) REVERT: B 357 GLN cc_start: 0.7331 (mt0) cc_final: 0.6544 (pp30) REVERT: B 433 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7990 (t) REVERT: B 467 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8189 (mptt) REVERT: B 738 TYR cc_start: 0.8038 (t80) cc_final: 0.7822 (t80) REVERT: C 91 LEU cc_start: 0.8793 (pt) cc_final: 0.8186 (tp) REVERT: C 767 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9130 (pp) REVERT: C 775 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: D 357 GLN cc_start: 0.7283 (mt0) cc_final: 0.6722 (pp30) REVERT: D 433 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7905 (t) REVERT: D 467 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8212 (mptt) REVERT: D 702 MET cc_start: 0.6966 (mmt) cc_final: 0.6683 (mmt) REVERT: D 795 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9275 (tt) outliers start: 121 outliers final: 94 residues processed: 348 average time/residue: 0.2524 time to fit residues: 147.8313 Evaluate side-chains 346 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 247 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 775 PHE Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 818 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 314 optimal weight: 0.6980 chunk 289 optimal weight: 0.8980 chunk 250 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 193 optimal weight: 50.0000 chunk 153 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN D 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 21156 Z= 0.468 Angle : 0.743 15.106 29196 Z= 0.387 Chirality : 0.047 0.221 3782 Planarity : 0.004 0.043 3706 Dihedral : 5.908 56.825 3283 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.75 % Favored : 90.18 % Rotamer: Outliers : 6.22 % Allowed : 21.71 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.36 (0.15), residues: 3148 helix: 0.85 (0.15), residues: 1312 sheet: -1.75 (0.26), residues: 380 loop : -2.39 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 559 HIS 0.007 0.002 HIS A 801 PHE 0.033 0.002 PHE C 554 TYR 0.021 0.002 TYR A 668 ARG 0.004 0.001 ARG D 774 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 249 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8753 (pt) cc_final: 0.8183 (tp) REVERT: A 776 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7510 (mmm-85) REVERT: B 186 ILE cc_start: 0.9250 (pt) cc_final: 0.8943 (tp) REVERT: B 240 ILE cc_start: 0.8459 (tp) cc_final: 0.8206 (mt) REVERT: B 357 GLN cc_start: 0.7289 (mt0) cc_final: 0.6615 (pp30) REVERT: B 433 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7936 (t) REVERT: B 467 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8190 (mptt) REVERT: B 739 MET cc_start: 0.6826 (mtt) cc_final: 0.6527 (mtt) REVERT: C 91 LEU cc_start: 0.8845 (pt) cc_final: 0.8339 (tp) REVERT: C 767 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9129 (pp) REVERT: D 357 GLN cc_start: 0.7446 (mt0) cc_final: 0.6958 (pp30) REVERT: D 433 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7872 (t) REVERT: D 467 LYS cc_start: 0.8772 (mmmt) cc_final: 0.8193 (mptt) REVERT: D 702 MET cc_start: 0.7106 (mmt) cc_final: 0.6853 (mmt) REVERT: D 795 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9295 (tm) outliers start: 106 outliers final: 93 residues processed: 336 average time/residue: 0.2484 time to fit residues: 141.3513 Evaluate side-chains 336 residues out of total 2760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 239 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 813 TRP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 818 MET Chi-restraints excluded: chain D residue 841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 231 optimal weight: 0.0670 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 251 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 257 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 0.0010 chunk 220 optimal weight: 10.0000 overall best weight: 1.3326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 697 ASN C 162 HIS D 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.179900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.152373 restraints weight = 45207.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.143121 restraints weight = 53195.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.140260 restraints weight = 54937.339| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21156 Z= 0.228 Angle : 0.628 11.926 29196 Z= 0.318 Chirality : 0.044 0.163 3782 Planarity : 0.004 0.044 3706 Dihedral : 5.424 57.903 3281 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 5.75 % Allowed : 22.18 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3148 helix: 1.20 (0.15), residues: 1308 sheet: -1.65 (0.26), residues: 388 loop : -2.29 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 584 HIS 0.003 0.001 HIS C 592 PHE 0.023 0.002 PHE D 637 TYR 0.022 0.001 TYR D 239 ARG 0.002 0.000 ARG D 774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4012.05 seconds wall clock time: 77 minutes 11.49 seconds (4631.49 seconds total)