Starting phenix.real_space_refine on Wed Aug 7 09:13:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bib_44586/08_2024/9bib_44586.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bib_44586/08_2024/9bib_44586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bib_44586/08_2024/9bib_44586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bib_44586/08_2024/9bib_44586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bib_44586/08_2024/9bib_44586.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bib_44586/08_2024/9bib_44586.cif" } resolution = 3.81 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 174 atoms to isotropic. 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 80 5.16 5 C 12236 2.51 5 N 3414 2.21 5 O 3539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 468": "NH1" <-> "NH2" Residue "A PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C ARG 722": "NH1" <-> "NH2" Residue "D ARG 540": "NH1" <-> "NH2" Residue "D PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 19269 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 4886 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1824 Unresolved non-hydrogen dihedrals: 1176 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 26, 'ASP:plan': 29, 'TYR:plan': 11, 'ASN:plan1': 29, 'TRP:plan': 1, 'HIS:plan': 13, 'PHE:plan': 8, 'GLU:plan': 46, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 841 Chain: "B" Number of atoms: 4733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 4733 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 431} Link IDs: {'PTRANS': 29, 'TRANS': 759} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1571 Unresolved non-hydrogen angles: 2003 Unresolved non-hydrogen dihedrals: 1313 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 21, 'ASP:plan': 45, 'TYR:plan': 19, 'ASN:plan1': 24, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 18, 'GLU:plan': 45, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 915 Chain: "C" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 4885 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1452 Unresolved non-hydrogen angles: 1824 Unresolved non-hydrogen dihedrals: 1178 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 26, 'ASP:plan': 29, 'TYR:plan': 11, 'ASN:plan1': 29, 'TRP:plan': 1, 'HIS:plan': 13, 'PHE:plan': 8, 'GLU:plan': 46, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 841 Chain: "D" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 4735 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 431} Link IDs: {'PTRANS': 29, 'TRANS': 759} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1568 Unresolved non-hydrogen angles: 1999 Unresolved non-hydrogen dihedrals: 1309 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 45, 'TYR:plan': 19, 'ASN:plan1': 24, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 17, 'GLU:plan': 45, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 913 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} 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: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 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: 12.09, per 1000 atoms: 0.63 Number of scatterers: 19269 At special positions: 0 Unit cell: (125.706, 149.814, 185.115, 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 80 16.00 O 3539 8.00 N 3414 7.00 C 12236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " 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: 7.58 Conformation dependent library (CDL) restraints added in 4.5 seconds 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5920 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 28 sheets defined 44.4% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.696A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 4.248A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.702A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.806A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.972A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 277 through 296 removed outlier: 3.590A pdb=" N ILE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 327 removed outlier: 4.589A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.668A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.529A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 654 removed outlier: 3.734A pdb=" N PHE A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 694 Processing helix chain 'A' and resid 695 through 698 removed outlier: 6.069A pdb=" N GLU A 698 " --> pdb=" O ARG A 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 695 through 698' Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 766 through 780 removed outlier: 4.012A pdb=" N GLN A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 811 through 841 removed outlier: 4.205A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.549A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 4.302A pdb=" N ALA B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 176 through 192 Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.589A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.284A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 264' Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.922A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 330' Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.528A pdb=" N ASN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.655A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 581 Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.574A pdb=" N LEU B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 647 Processing helix chain 'B' and resid 649 through 654 Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.385A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.704A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 844 removed outlier: 3.815A pdb=" N TYR B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET B 824 " --> pdb=" O GLY B 820 " (cutoff:3.500A) removed outlier: 3.819A 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 86 Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.740A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 158 removed outlier: 4.259A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.716A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.793A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 260 removed outlier: 3.971A pdb=" N LEU C 259 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 260 " --> pdb=" O ASN C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 260' Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.558A pdb=" N ILE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 327 removed outlier: 4.472A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.799A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.763A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 655 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 694 Processing helix chain 'C' and resid 695 through 698 removed outlier: 6.128A pdb=" N GLU C 698 " --> pdb=" O ARG C 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 695 through 698' Processing helix chain 'C' and resid 699 through 708 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 766 through 780 removed outlier: 3.630A pdb=" N GLN C 770 " --> pdb=" O SER C 766 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 811 through 840 removed outlier: 4.029A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 Processing helix chain 'D' and resid 77 through 92 removed outlier: 4.223A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.305A pdb=" N ALA D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 176 through 192 removed outlier: 3.698A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.581A pdb=" N LYS D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.810A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR D 330 " --> pdb=" O LYS D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 330' Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.521A pdb=" N ASN D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.527A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 516 through 523 Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 555 through 581 Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.770A pdb=" N ASN D 615 " --> pdb=" O GLY D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 647 Processing helix chain 'D' and resid 649 through 654 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 771 through 787 removed outlier: 4.381A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.578A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 819 removed outlier: 3.525A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 844 removed outlier: 3.612A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 7.109A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 7.207A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.794A pdb=" N GLY A 268 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 354 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 478 removed outlier: 7.225A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.667A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.606A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 542 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 73 removed outlier: 8.447A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY B 36 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE B 123 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL B 97 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY B 125 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE B 99 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N HIS B 127 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 101 " --> pdb=" O HIS B 127 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 203 removed outlier: 8.216A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 231 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 362 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 476 through 480 removed outlier: 3.602A pdb=" N THR B 410 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER B 407 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 420 removed outlier: 3.974A pdb=" N ILE B 453 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 488 through 490 removed outlier: 4.149A pdb=" N LYS B 488 " --> pdb=" O ASN B 495 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 495 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 490 " --> pdb=" O THR B 493 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.046A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.046A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 64 through 65 removed outlier: 7.044A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.187A pdb=" N ILE C 163 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 267 through 268 removed outlier: 3.785A pdb=" N GLY C 268 " --> pdb=" O MET C 354 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.071A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.675A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 412 " --> pdb=" O CYS C 454 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 487 through 488 removed outlier: 3.578A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.587A pdb=" N ALA C 682 " --> pdb=" O ALA C 728 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 729 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 70 through 73 removed outlier: 8.399A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY D 36 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE D 123 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL D 97 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY D 125 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE D 99 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N HIS D 127 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D 101 " --> pdb=" O HIS D 127 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 203 removed outlier: 8.251A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 279 " --> pdb=" O ILE D 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 362 " --> pdb=" O TRP D 379 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 476 through 480 removed outlier: 6.928A pdb=" N LEU D 406 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N TYR D 479 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.971A pdb=" N ILE D 453 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 488 through 490 removed outlier: 4.085A pdb=" N LYS D 488 " --> pdb=" O ASN D 495 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN D 495 " --> pdb=" O LYS D 488 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 490 " --> pdb=" O THR D 493 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.932A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.932A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 3057 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: 8.01 Time building geometry restraints manager: 8.34 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: 3293 1.25 - 1.39: 4580 1.39 - 1.53: 10888 1.53 - 1.68: 683 1.68 - 1.82: 132 Bond restraints: 19576 Sorted by residual: bond pdb=" C PRO B 623 " pdb=" N LYS B 624 " ideal model delta sigma weight residual 1.331 1.587 -0.256 1.51e-02 4.39e+03 2.87e+02 bond pdb=" CA SER B 617 " pdb=" CB SER B 617 " ideal model delta sigma weight residual 1.539 1.371 0.168 1.20e-02 6.94e+03 1.96e+02 bond pdb=" C VAL D 618 " pdb=" O VAL D 618 " ideal model delta sigma weight residual 1.240 1.108 0.131 1.26e-02 6.30e+03 1.09e+02 bond pdb=" C PHE D 614 " pdb=" O PHE D 614 " ideal model delta sigma weight residual 1.237 1.114 0.123 1.19e-02 7.06e+03 1.06e+02 bond pdb=" CA SER D 617 " pdb=" CB SER D 617 " ideal model delta sigma weight residual 1.538 1.423 0.115 1.35e-02 5.49e+03 7.31e+01 ... (remaining 19571 not shown) Histogram of bond angle deviations from ideal: 90.64 - 100.03: 4 100.03 - 109.41: 1404 109.41 - 118.80: 14179 118.80 - 128.18: 11276 128.18 - 137.57: 121 Bond angle restraints: 26984 Sorted by residual: angle pdb=" CA PHE D 614 " pdb=" C PHE D 614 " pdb=" O PHE D 614 " ideal model delta sigma weight residual 120.42 107.93 12.49 1.06e+00 8.90e-01 1.39e+02 angle pdb=" CA PHE D 614 " pdb=" CB PHE D 614 " pdb=" CG PHE D 614 " ideal model delta sigma weight residual 113.80 102.76 11.04 1.00e+00 1.00e+00 1.22e+02 angle pdb=" C LEU B 612 " pdb=" N VAL B 613 " pdb=" CA VAL B 613 " ideal model delta sigma weight residual 121.77 107.02 14.75 1.44e+00 4.82e-01 1.05e+02 angle pdb=" C ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta sigma weight residual 110.42 90.64 19.78 1.99e+00 2.53e-01 9.88e+01 angle pdb=" C LEU D 612 " pdb=" N VAL D 613 " pdb=" CA VAL D 613 " ideal model delta sigma weight residual 121.35 105.90 15.45 1.58e+00 4.01e-01 9.56e+01 ... (remaining 26979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 10839 11.99 - 23.99: 285 23.99 - 35.98: 92 35.98 - 47.98: 37 47.98 - 59.97: 12 Dihedral angle restraints: 11265 sinusoidal: 2137 harmonic: 9128 Sorted by residual: dihedral pdb=" C ASN D 615 " pdb=" N ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta harmonic sigma weight residual -122.60 -95.95 -26.65 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C PHE C 654 " pdb=" N PHE C 654 " pdb=" CA PHE C 654 " pdb=" CB PHE C 654 " ideal model delta harmonic sigma weight residual -122.60 -149.01 26.41 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" N PHE C 654 " pdb=" C PHE C 654 " pdb=" CA PHE C 654 " pdb=" CB PHE C 654 " ideal model delta harmonic sigma weight residual 122.80 146.14 -23.34 0 2.50e+00 1.60e-01 8.72e+01 ... (remaining 11262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 3398 0.207 - 0.414: 13 0.414 - 0.621: 2 0.621 - 0.828: 1 0.828 - 1.036: 3 Chirality restraints: 3417 Sorted by residual: chirality pdb=" CA PHE C 654 " pdb=" N PHE C 654 " pdb=" C PHE C 654 " pdb=" CB PHE C 654 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.68e+01 chirality pdb=" CA SER D 617 " pdb=" N SER D 617 " pdb=" C SER D 617 " pdb=" CB SER D 617 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA PHE D 614 " pdb=" N PHE D 614 " pdb=" C PHE D 614 " pdb=" CB PHE D 614 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.05e+01 ... (remaining 3414 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 614 " 0.023 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C PHE D 614 " -0.090 2.00e-02 2.50e+03 pdb=" O PHE D 614 " 0.034 2.00e-02 2.50e+03 pdb=" N ASN D 615 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 619 " 0.025 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C PRO D 619 " -0.090 2.00e-02 2.50e+03 pdb=" O PRO D 619 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL D 620 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 643 " -0.021 2.00e-02 2.50e+03 4.44e-02 1.98e+01 pdb=" C LEU D 643 " 0.077 2.00e-02 2.50e+03 pdb=" O LEU D 643 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA D 644 " -0.027 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1519 2.74 - 3.28: 18228 3.28 - 3.82: 29862 3.82 - 4.36: 27331 4.36 - 4.90: 52467 Nonbonded interactions: 129407 Sorted by model distance: nonbonded pdb=" O THR B 647 " pdb=" OG1 THR B 647 " model vdw 2.200 3.040 nonbonded pdb=" O LEU D 612 " pdb=" CA VAL D 613 " model vdw 2.263 2.776 nonbonded pdb=" O LEU B 612 " pdb=" CA VAL B 613 " model vdw 2.282 2.776 nonbonded pdb=" OE1 GLU D 413 " pdb=" OG SER D 512 " model vdw 2.303 3.040 nonbonded pdb=" CB ASN D 615 " pdb=" N ASN D 616 " model vdw 2.309 2.816 ... (remaining 129402 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' and (resid 25 through 789 or (resid 790 and (name N or name CA or nam \ e C or name O or name CB )) or resid 791 through 831 or (resid 832 and (name N o \ r name CA or name C or name O or name CB )) or resid 833 through 841 or resid 10 \ 01)) selection = (chain 'C' and (resid 25 through 816 or (resid 817 through 819 and (name N or na \ me CA or name C or name O or name CB )) or resid 820 through 841 or resid 1001)) \ } ncs_group { reference = (chain 'B' and (resid 34 through 576 or (resid 577 through 581 and (name N or na \ me CA or name C or name O or name CB )) or resid 582 through 655 or (resid 656 t \ hrough 658 and (name N or name CA or name C or name O or name CB )) or resid 659 \ through 844 or resid 1001)) selection = (chain 'D' and (resid 34 through 562 or (resid 563 and (name N or name CA or nam \ e C or name O or name CB )) or resid 564 through 835 or (resid 836 and (name N o \ r name CA or name C or name O or name CB )) or resid 837 through 844 or resid 10 \ 01)) } 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 56.130 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 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 : 0.004 0.256 19576 Z= 0.287 Angle : 0.625 19.781 26984 Z= 0.413 Chirality : 0.055 1.036 3417 Planarity : 0.004 0.095 3552 Dihedral : 7.502 59.972 5309 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 4.65 % Allowed : 7.43 % Favored : 87.92 % Cbeta Deviations : 0.41 % 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: -2.18 (0.13), residues: 3144 helix: -0.02 (0.13), residues: 1352 sheet: -1.28 (0.28), residues: 312 loop : -2.96 (0.13), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP C 636 HIS 0.001 0.000 HIS D 703 PHE 0.072 0.001 PHE D 614 TYR 0.004 0.000 TYR D 731 ARG 0.001 0.000 ARG D 519 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 402 time to evaluate : 2.253 Fit side-chains REVERT: A 807 THR cc_start: 0.8184 (t) cc_final: 0.7922 (m) REVERT: B 607 TRP cc_start: 0.7682 (t-100) cc_final: 0.5152 (t60) REVERT: B 823 TYR cc_start: 0.6946 (m-80) cc_final: 0.6717 (m-10) REVERT: C 166 LEU cc_start: 0.8403 (tt) cc_final: 0.8195 (mp) REVERT: C 584 SER cc_start: 0.5077 (t) cc_final: 0.4755 (p) REVERT: D 628 SER cc_start: 0.7181 (p) cc_final: 0.6877 (t) outliers start: 50 outliers final: 17 residues processed: 434 average time/residue: 0.2795 time to fit residues: 192.5010 Evaluate side-chains 258 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 241 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 50.0000 chunk 237 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 246 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 149 optimal weight: 1.9990 chunk 183 optimal weight: 40.0000 chunk 285 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS A 771 GLN B 615 ASN B 703 HIS C 405 GLN C 477 HIS C 509 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19576 Z= 0.267 Angle : 0.536 8.499 26984 Z= 0.293 Chirality : 0.044 0.171 3417 Planarity : 0.004 0.056 3552 Dihedral : 4.085 58.656 3263 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 6.60 % Allowed : 15.33 % Favored : 78.07 % 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: -0.88 (0.15), residues: 3144 helix: 1.27 (0.14), residues: 1361 sheet: -0.80 (0.29), residues: 338 loop : -2.48 (0.14), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 498 HIS 0.009 0.002 HIS A 780 PHE 0.042 0.003 PHE A 533 TYR 0.023 0.002 TYR C 410 ARG 0.008 0.001 ARG D 505 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 255 time to evaluate : 2.064 Fit side-chains REVERT: A 544 LYS cc_start: 0.6652 (OUTLIER) cc_final: 0.6297 (mtpp) REVERT: A 607 MET cc_start: 0.7833 (tpp) cc_final: 0.7446 (tpp) REVERT: B 567 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7742 (mt) REVERT: B 607 TRP cc_start: 0.8390 (t-100) cc_final: 0.8077 (t60) REVERT: B 631 MET cc_start: 0.8150 (tpt) cc_final: 0.7875 (tpt) REVERT: D 476 TYR cc_start: 0.7387 (p90) cc_final: 0.7176 (p90) REVERT: D 628 SER cc_start: 0.7310 (p) cc_final: 0.7048 (t) outliers start: 71 outliers final: 37 residues processed: 304 average time/residue: 0.2212 time to fit residues: 114.1684 Evaluate side-chains 256 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 217 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 768 LYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 50.0000 chunk 88 optimal weight: 40.0000 chunk 237 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 308 optimal weight: 0.9980 chunk 254 optimal weight: 50.0000 chunk 283 optimal weight: 0.3980 chunk 97 optimal weight: 50.0000 chunk 229 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 486 HIS C 705 HIS D 662 GLN D 703 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19576 Z= 0.169 Angle : 0.460 8.281 26984 Z= 0.249 Chirality : 0.042 0.151 3417 Planarity : 0.003 0.054 3552 Dihedral : 3.569 54.226 3248 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 4.93 % Allowed : 16.82 % Favored : 78.25 % 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: -0.25 (0.15), residues: 3144 helix: 1.87 (0.15), residues: 1363 sheet: -0.73 (0.28), residues: 342 loop : -2.17 (0.14), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 607 HIS 0.005 0.001 HIS A 780 PHE 0.025 0.002 PHE D 114 TYR 0.022 0.001 TYR A 681 ARG 0.005 0.001 ARG A 722 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 254 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.6163 (mtpp) REVERT: A 607 MET cc_start: 0.7794 (tpp) cc_final: 0.7397 (tpp) REVERT: B 607 TRP cc_start: 0.8439 (t-100) cc_final: 0.8001 (t60) REVERT: B 705 TYR cc_start: 0.7473 (t80) cc_final: 0.7059 (t80) REVERT: D 476 TYR cc_start: 0.7382 (p90) cc_final: 0.7119 (p90) REVERT: D 554 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7394 (m-10) REVERT: D 614 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8032 (m-80) outliers start: 53 outliers final: 33 residues processed: 291 average time/residue: 0.2217 time to fit residues: 110.0019 Evaluate side-chains 261 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 614 PHE Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 0.0870 chunk 214 optimal weight: 8.9990 chunk 148 optimal weight: 0.0070 chunk 31 optimal weight: 30.0000 chunk 136 optimal weight: 0.6980 chunk 191 optimal weight: 9.9990 chunk 286 optimal weight: 0.2980 chunk 303 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 81 optimal weight: 50.0000 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 662 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19576 Z= 0.120 Angle : 0.429 7.763 26984 Z= 0.230 Chirality : 0.041 0.161 3417 Planarity : 0.003 0.058 3552 Dihedral : 3.363 52.189 3248 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.80 % Rotamer: Outliers : 5.48 % Allowed : 17.38 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.15 (0.16), residues: 3144 helix: 2.18 (0.15), residues: 1361 sheet: -0.59 (0.29), residues: 355 loop : -1.91 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 607 HIS 0.002 0.001 HIS C 67 PHE 0.026 0.001 PHE D 114 TYR 0.015 0.001 TYR A 681 ARG 0.005 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 241 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7551 (tm) REVERT: A 607 MET cc_start: 0.7768 (tpp) cc_final: 0.7392 (tpp) REVERT: B 567 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7682 (mt) REVERT: B 705 TYR cc_start: 0.7534 (t80) cc_final: 0.7087 (t80) REVERT: D 476 TYR cc_start: 0.7245 (p90) cc_final: 0.7041 (p90) REVERT: D 554 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7388 (m-10) REVERT: D 614 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7924 (m-80) outliers start: 59 outliers final: 38 residues processed: 284 average time/residue: 0.2211 time to fit residues: 107.1477 Evaluate side-chains 269 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 227 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 614 PHE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 4 optimal weight: 40.0000 chunk 225 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 259 optimal weight: 0.5980 chunk 209 optimal weight: 0.0070 chunk 0 optimal weight: 70.0000 chunk 154 optimal weight: 10.0000 chunk 272 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN D 662 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19576 Z= 0.221 Angle : 0.494 8.871 26984 Z= 0.268 Chirality : 0.043 0.169 3417 Planarity : 0.003 0.060 3552 Dihedral : 3.696 49.102 3248 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 6.60 % Allowed : 17.94 % Favored : 75.46 % 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: 0.20 (0.16), residues: 3144 helix: 2.20 (0.15), residues: 1364 sheet: -0.59 (0.29), residues: 351 loop : -1.85 (0.15), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 607 HIS 0.004 0.001 HIS A 780 PHE 0.033 0.002 PHE A 533 TYR 0.016 0.001 TYR C 410 ARG 0.006 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 230 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7576 (tm) REVERT: A 607 MET cc_start: 0.7921 (tpp) cc_final: 0.7483 (tpp) REVERT: A 693 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.6592 (t80) REVERT: B 567 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7835 (mt) REVERT: B 705 TYR cc_start: 0.7539 (t80) cc_final: 0.7165 (t80) REVERT: C 762 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6645 (mtp) REVERT: D 476 TYR cc_start: 0.7572 (p90) cc_final: 0.7313 (p90) REVERT: D 554 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7493 (m-10) outliers start: 71 outliers final: 49 residues processed: 281 average time/residue: 0.2178 time to fit residues: 106.0277 Evaluate side-chains 273 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 219 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 614 PHE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 0.0060 chunk 273 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 252 optimal weight: 0.7980 chunk 140 optimal weight: 0.2980 chunk 25 optimal weight: 20.0000 chunk 100 optimal weight: 50.0000 chunk 159 optimal weight: 50.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS D 486 HIS D 662 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19576 Z= 0.131 Angle : 0.446 10.616 26984 Z= 0.237 Chirality : 0.041 0.159 3417 Planarity : 0.003 0.061 3552 Dihedral : 3.432 47.973 3248 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 5.67 % Allowed : 19.33 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.43 (0.16), residues: 3144 helix: 2.33 (0.15), residues: 1364 sheet: -0.35 (0.29), residues: 352 loop : -1.69 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 607 HIS 0.002 0.001 HIS D 703 PHE 0.025 0.001 PHE B 554 TYR 0.012 0.001 TYR A 681 ARG 0.006 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 238 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7697 (mmt) cc_final: 0.6963 (mpp) REVERT: A 568 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7457 (tm) REVERT: A 607 MET cc_start: 0.7847 (tpp) cc_final: 0.7386 (tpp) REVERT: A 693 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6558 (t80) REVERT: A 709 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.5160 (p90) REVERT: B 567 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7768 (mt) REVERT: B 705 TYR cc_start: 0.7513 (t80) cc_final: 0.7220 (t80) REVERT: D 554 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7543 (m-10) outliers start: 61 outliers final: 44 residues processed: 283 average time/residue: 0.2169 time to fit residues: 106.6667 Evaluate side-chains 269 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 220 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 0.0570 chunk 34 optimal weight: 40.0000 chunk 173 optimal weight: 0.4980 chunk 221 optimal weight: 0.0970 chunk 171 optimal weight: 20.0000 chunk 255 optimal weight: 50.0000 chunk 169 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19576 Z= 0.167 Angle : 0.463 9.107 26984 Z= 0.246 Chirality : 0.042 0.176 3417 Planarity : 0.003 0.065 3552 Dihedral : 3.458 46.807 3247 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 5.67 % Allowed : 19.70 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.50 (0.16), residues: 3144 helix: 2.40 (0.15), residues: 1359 sheet: -0.36 (0.29), residues: 357 loop : -1.64 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 610 HIS 0.003 0.001 HIS A 780 PHE 0.030 0.002 PHE D 114 TYR 0.021 0.001 TYR D 705 ARG 0.007 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 226 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7695 (mmt) cc_final: 0.6980 (mpp) REVERT: A 568 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7487 (tm) REVERT: A 607 MET cc_start: 0.7862 (tpp) cc_final: 0.7392 (tpp) REVERT: A 693 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6561 (t80) REVERT: A 709 HIS cc_start: 0.6838 (OUTLIER) cc_final: 0.5189 (p90) REVERT: B 567 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7816 (mt) REVERT: B 705 TYR cc_start: 0.7569 (t80) cc_final: 0.7313 (t80) REVERT: D 134 MET cc_start: 0.6665 (tpt) cc_final: 0.5659 (tpt) REVERT: D 554 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7530 (m-10) REVERT: D 609 LEU cc_start: 0.8726 (mt) cc_final: 0.8474 (mt) outliers start: 61 outliers final: 48 residues processed: 271 average time/residue: 0.2119 time to fit residues: 99.9922 Evaluate side-chains 268 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 215 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 50.0000 chunk 120 optimal weight: 0.6980 chunk 180 optimal weight: 7.9990 chunk 91 optimal weight: 30.0000 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 192 optimal weight: 20.0000 chunk 206 optimal weight: 0.4980 chunk 149 optimal weight: 4.9990 chunk 28 optimal weight: 0.0170 chunk 237 optimal weight: 4.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19576 Z= 0.132 Angle : 0.450 8.591 26984 Z= 0.237 Chirality : 0.042 0.174 3417 Planarity : 0.003 0.066 3552 Dihedral : 3.362 45.556 3247 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 5.48 % Allowed : 20.63 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.62 (0.16), residues: 3144 helix: 2.48 (0.15), residues: 1355 sheet: -0.27 (0.29), residues: 355 loop : -1.54 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 610 HIS 0.003 0.001 HIS D 703 PHE 0.025 0.001 PHE B 554 TYR 0.021 0.001 TYR D 705 ARG 0.006 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 227 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7760 (mmt) cc_final: 0.7097 (mpp) REVERT: A 568 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7459 (tm) REVERT: A 607 MET cc_start: 0.7818 (tpp) cc_final: 0.7339 (tpp) REVERT: A 693 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.6524 (t80) REVERT: A 709 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.5446 (p90) REVERT: B 567 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7748 (mt) REVERT: D 134 MET cc_start: 0.6634 (tpt) cc_final: 0.5631 (tpt) REVERT: D 554 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7487 (m-10) outliers start: 59 outliers final: 47 residues processed: 271 average time/residue: 0.2163 time to fit residues: 102.9766 Evaluate side-chains 270 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 218 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 0.8980 chunk 289 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 282 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 254 optimal weight: 40.0000 chunk 266 optimal weight: 50.0000 chunk 281 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19576 Z= 0.155 Angle : 0.467 9.082 26984 Z= 0.247 Chirality : 0.042 0.182 3417 Planarity : 0.003 0.070 3552 Dihedral : 3.430 44.696 3247 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 5.20 % Allowed : 21.10 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.16), residues: 3144 helix: 2.49 (0.15), residues: 1357 sheet: 0.03 (0.30), residues: 332 loop : -1.52 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 607 HIS 0.003 0.001 HIS A 404 PHE 0.029 0.001 PHE B 554 TYR 0.021 0.001 TYR D 705 ARG 0.005 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 222 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7677 (mmt) cc_final: 0.7054 (mpp) REVERT: A 568 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7466 (tm) REVERT: A 607 MET cc_start: 0.7826 (tpp) cc_final: 0.7353 (tpp) REVERT: A 693 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6537 (t80) REVERT: A 709 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.5372 (p90) REVERT: B 567 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7742 (mt) REVERT: C 679 PHE cc_start: 0.4382 (OUTLIER) cc_final: 0.4072 (t80) REVERT: D 134 MET cc_start: 0.6622 (tpt) cc_final: 0.5656 (tpt) REVERT: D 554 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7484 (m-10) REVERT: D 609 LEU cc_start: 0.8744 (mt) cc_final: 0.8509 (mt) outliers start: 56 outliers final: 45 residues processed: 267 average time/residue: 0.2180 time to fit residues: 102.3911 Evaluate side-chains 265 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 214 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 50.0000 chunk 298 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 207 optimal weight: 0.0980 chunk 312 optimal weight: 0.9990 chunk 287 optimal weight: 1.9990 chunk 249 optimal weight: 8.9990 chunk 25 optimal weight: 40.0000 chunk 192 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS D 662 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19576 Z= 0.326 Angle : 0.582 11.133 26984 Z= 0.312 Chirality : 0.045 0.192 3417 Planarity : 0.004 0.071 3552 Dihedral : 4.144 43.848 3247 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 5.30 % Allowed : 21.10 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.40 (0.16), residues: 3144 helix: 2.14 (0.15), residues: 1366 sheet: -0.19 (0.30), residues: 328 loop : -1.56 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 768 HIS 0.008 0.002 HIS C 477 PHE 0.042 0.002 PHE B 554 TYR 0.042 0.002 TYR B 705 ARG 0.006 0.001 ARG A 523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 215 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7816 (mmt) cc_final: 0.7166 (mpp) REVERT: A 568 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7504 (tm) REVERT: A 607 MET cc_start: 0.8031 (tpp) cc_final: 0.7505 (tpp) REVERT: A 693 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6910 (t80) REVERT: A 709 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.5625 (p90) REVERT: B 567 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7970 (mt) REVERT: C 679 PHE cc_start: 0.4420 (OUTLIER) cc_final: 0.4008 (t80) REVERT: D 134 MET cc_start: 0.6519 (tpt) cc_final: 0.5675 (tpt) REVERT: D 554 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7572 (m-10) REVERT: D 609 LEU cc_start: 0.8829 (mt) cc_final: 0.8567 (mt) REVERT: D 631 MET cc_start: 0.6469 (mmm) cc_final: 0.6104 (tpt) outliers start: 57 outliers final: 41 residues processed: 260 average time/residue: 0.2406 time to fit residues: 109.7483 Evaluate side-chains 255 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 208 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.3980 chunk 265 optimal weight: 0.0370 chunk 76 optimal weight: 4.9990 chunk 229 optimal weight: 0.0070 chunk 36 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 249 optimal weight: 0.0670 chunk 104 optimal weight: 20.0000 chunk 256 optimal weight: 50.0000 chunk 31 optimal weight: 50.0000 chunk 45 optimal weight: 5.9990 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.177871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.158529 restraints weight = 37463.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.153147 restraints weight = 46224.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152225 restraints weight = 52716.375| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19576 Z= 0.133 Angle : 0.475 10.453 26984 Z= 0.251 Chirality : 0.042 0.187 3417 Planarity : 0.003 0.080 3552 Dihedral : 3.560 42.596 3247 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 3.44 % Allowed : 22.96 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.70 (0.16), residues: 3144 helix: 2.39 (0.15), residues: 1360 sheet: -0.02 (0.30), residues: 350 loop : -1.40 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 607 HIS 0.004 0.001 HIS A 404 PHE 0.030 0.001 PHE B 554 TYR 0.032 0.001 TYR B 705 ARG 0.006 0.001 ARG A 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3467.56 seconds wall clock time: 61 minutes 57.86 seconds (3717.86 seconds total)