Starting phenix.real_space_refine on Wed Aug 7 08:57:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9are_43779/08_2024/9are_43779.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9are_43779/08_2024/9are_43779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9are_43779/08_2024/9are_43779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9are_43779/08_2024/9are_43779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9are_43779/08_2024/9are_43779.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9are_43779/08_2024/9are_43779.cif" } resolution = 3.72 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= 0.018 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 12190 2.51 5 N 3414 2.21 5 O 3538 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 ARG 694": "NH1" <-> "NH2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B PHE 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C GLU 781": "OE1" <-> "OE2" Residue "C PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 517": "OE1" <-> "OE2" Residue "D GLU 531": "OE1" <-> "OE2" Residue "D PHE 822": "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: 19222 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 4880 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1458 Unresolved non-hydrogen angles: 1832 Unresolved non-hydrogen dihedrals: 1184 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 29, 'TYR:plan': 11, 'ASN:plan1': 29, 'TRP:plan': 1, 'HIS:plan': 13, 'PHE:plan': 9, 'GLU:plan': 46, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 843 Chain: "B" Number of atoms: 4716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 4716 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 434} Link IDs: {'PTRANS': 29, 'TRANS': 759} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1590 Unresolved non-hydrogen angles: 2028 Unresolved non-hydrogen dihedrals: 1331 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 45, 'TYR:plan': 20, 'ASN:plan1': 24, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 19, 'GLU:plan': 45, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 932 Chain: "C" Number of atoms: 4880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 4880 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1458 Unresolved non-hydrogen angles: 1832 Unresolved non-hydrogen dihedrals: 1184 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 29, 'TYR:plan': 11, 'ASN:plan1': 29, 'TRP:plan': 1, 'HIS:plan': 13, 'PHE:plan': 9, 'GLU:plan': 46, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 843 Chain: "D" Number of atoms: 4716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 4716 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 434} Link IDs: {'PTRANS': 29, 'TRANS': 759} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1590 Unresolved non-hydrogen angles: 2028 Unresolved non-hydrogen dihedrals: 1331 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 45, 'TYR:plan': 20, 'ASN:plan1': 24, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 19, 'GLU:plan': 45, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 932 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: 12.31, per 1000 atoms: 0.64 Number of scatterers: 19222 At special positions: 0 Unit cell: (150.675, 133.455, 181.671, 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 3538 8.00 N 3414 7.00 C 12190 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=2.02 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=2.02 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: 7.77 Conformation dependent library (CDL) restraints added in 4.2 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 44.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.616A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 103 through 112 removed outlier: 4.069A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.876A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 4.011A 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: 3.653A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.765A 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 261 removed outlier: 4.064A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 296 removed outlier: 3.804A pdb=" N ILE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 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 527 removed outlier: 4.125A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.622A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.845A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 655 removed outlier: 3.617A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (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 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 707 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: 4.097A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 822 through 840 removed outlier: 3.929A pdb=" N ALA A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.531A pdb=" N ASP B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 4.015A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 4.320A pdb=" N ALA B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 176 through 192 removed outlier: 3.888A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.642A 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 288 through 311 Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.989A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 4.191A 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: 3.621A pdb=" N ASN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.826A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 555 through 581 Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.570A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 646 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 removed outlier: 3.557A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.437A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.813A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 844 removed outlier: 4.053A pdb=" N MET B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET B 824 " --> pdb=" O GLY B 820 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.616A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'C' and resid 103 through 112 removed outlier: 4.068A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 158 removed outlier: 3.876A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 4.012A 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: 3.653A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.765A 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 261 removed outlier: 4.063A pdb=" N LEU C 259 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.804A pdb=" N ILE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 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 527 removed outlier: 4.125A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.622A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.845A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 655 removed outlier: 3.616A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 695 Processing helix chain 'C' and resid 696 through 698 No H-bonds generated for 'chain 'C' and resid 696 through 698' Processing helix chain 'C' and resid 699 through 707 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: 4.097A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 4.080A 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 812 through 822 Processing helix chain 'C' and resid 822 through 840 removed outlier: 3.929A pdb=" N ALA C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.531A pdb=" N ASP D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 4.015A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.320A 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: 3.888A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.642A 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: 3.989A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) removed outlier: 4.191A 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: 3.622A pdb=" N ASN D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.826A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 473 " --> pdb=" O SER D 469 " (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: 3.569A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 646 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 removed outlier: 3.557A pdb=" N ASN D 698 " --> pdb=" O ASN D 694 " (cutoff:3.500A) 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 752 through 754 No H-bonds generated for 'chain 'D' and resid 752 through 754' Processing helix chain 'D' and resid 771 through 787 removed outlier: 4.437A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.813A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 844 removed outlier: 4.053A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET D 824 " --> pdb=" O GLY D 820 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 825 " --> pdb=" O VAL D 821 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 3.767A pdb=" N VAL A 65 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 7.103A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 219 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 268 removed outlier: 3.576A pdb=" N MET A 354 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 478 removed outlier: 7.003A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.803A 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: 3.556A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.642A pdb=" N GLU A 528 " --> pdb=" O MET A 762 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.019A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 73 removed outlier: 6.750A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP B 101 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 42 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 128 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP B 101 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 144 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 203 removed outlier: 8.124A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 168 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU B 229 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.661A 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: 3.552A 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: 3.512A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 490 removed outlier: 4.078A 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: 3.934A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.934A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR B 532 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER B 759 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 65 removed outlier: 3.767A pdb=" N VAL C 65 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.103A pdb=" N ILE C 163 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 219 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 267 through 268 removed outlier: 3.576A pdb=" N MET C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.653A 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: 7.003A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.803A 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 412 removed outlier: 3.556A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 528 through 529 removed outlier: 3.642A pdb=" N GLU C 528 " --> pdb=" O MET C 762 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.019A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 67 through 73 removed outlier: 6.751A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 40 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP D 101 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 42 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY D 128 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP D 101 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 144 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 203 removed outlier: 8.124A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE D 168 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU D 229 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER D 279 " --> pdb=" O ILE D 365 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.661A 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: 3.551A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.511A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 489 through 490 removed outlier: 4.078A 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: 3.934A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.934A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR D 532 " --> pdb=" O SER D 759 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER D 759 " --> pdb=" O THR D 532 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.35 Time building geometry restraints manager: 8.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 56 1.21 - 1.36: 6669 1.36 - 1.52: 5633 1.52 - 1.67: 7032 1.67 - 1.82: 132 Bond restraints: 19522 Sorted by residual: bond pdb=" C LYS A 534 " pdb=" O LYS A 534 " ideal model delta sigma weight residual 1.235 1.060 0.175 1.26e-02 6.30e+03 1.93e+02 bond pdb=" C LYS C 534 " pdb=" O LYS C 534 " ideal model delta sigma weight residual 1.235 1.061 0.175 1.26e-02 6.30e+03 1.92e+02 bond pdb=" C PRO C 532 " pdb=" O PRO C 532 " ideal model delta sigma weight residual 1.233 1.076 0.157 1.24e-02 6.50e+03 1.61e+02 bond pdb=" C PRO A 532 " pdb=" O PRO A 532 " ideal model delta sigma weight residual 1.233 1.076 0.157 1.24e-02 6.50e+03 1.60e+02 bond pdb=" C PHE A 533 " pdb=" O PHE A 533 " ideal model delta sigma weight residual 1.236 1.066 0.170 1.39e-02 5.18e+03 1.50e+02 ... (remaining 19517 not shown) Histogram of bond angle deviations from ideal: 80.12 - 91.89: 4 91.89 - 103.65: 264 103.65 - 115.42: 11940 115.42 - 127.19: 14548 127.19 - 138.96: 158 Bond angle restraints: 26914 Sorted by residual: angle pdb=" CB MET C 762 " pdb=" CG MET C 762 " pdb=" SD MET C 762 " ideal model delta sigma weight residual 112.70 80.12 32.58 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CB MET A 762 " pdb=" CG MET A 762 " pdb=" SD MET A 762 " ideal model delta sigma weight residual 112.70 80.13 32.57 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C HIS A 780 " pdb=" CA HIS A 780 " pdb=" CB HIS A 780 " ideal model delta sigma weight residual 109.29 89.83 19.46 1.82e+00 3.02e-01 1.14e+02 angle pdb=" C HIS C 780 " pdb=" CA HIS C 780 " pdb=" CB HIS C 780 " ideal model delta sigma weight residual 109.29 89.85 19.44 1.82e+00 3.02e-01 1.14e+02 angle pdb=" CA PHE A 533 " pdb=" C PHE A 533 " pdb=" O PHE A 533 " ideal model delta sigma weight residual 119.32 108.56 10.76 1.19e+00 7.06e-01 8.17e+01 ... (remaining 26909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 10590 17.64 - 35.28: 502 35.28 - 52.92: 132 52.92 - 70.56: 16 70.56 - 88.20: 6 Dihedral angle restraints: 11246 sinusoidal: 2120 harmonic: 9126 Sorted by residual: dihedral pdb=" CB CYS A 744 " pdb=" SG CYS A 744 " pdb=" SG CYS A 798 " pdb=" CB CYS A 798 " ideal model delta sinusoidal sigma weight residual 93.00 -178.80 -88.20 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS C 744 " pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " pdb=" CB CYS C 798 " ideal model delta sinusoidal sigma weight residual 93.00 -178.83 -88.17 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" C HIS A 780 " pdb=" N HIS A 780 " pdb=" CA HIS A 780 " pdb=" CB HIS A 780 " ideal model delta harmonic sigma weight residual -122.60 -98.64 -23.96 0 2.50e+00 1.60e-01 9.18e+01 ... (remaining 11243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 3362 0.206 - 0.412: 36 0.412 - 0.619: 16 0.619 - 0.825: 0 0.825 - 1.031: 2 Chirality restraints: 3416 Sorted by residual: chirality pdb=" CA SER B 617 " pdb=" N SER B 617 " pdb=" C SER B 617 " pdb=" CB SER B 617 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.66e+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 1.48 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA LEU A 651 " pdb=" N LEU A 651 " pdb=" C LEU A 651 " pdb=" CB LEU A 651 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.80e+00 ... (remaining 3413 not shown) Planarity restraints: 3546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 609 " 0.034 2.00e-02 2.50e+03 6.83e-02 4.66e+01 pdb=" C LEU B 609 " -0.118 2.00e-02 2.50e+03 pdb=" O LEU B 609 " 0.044 2.00e-02 2.50e+03 pdb=" N TRP B 610 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 609 " -0.034 2.00e-02 2.50e+03 6.80e-02 4.63e+01 pdb=" C LEU D 609 " 0.118 2.00e-02 2.50e+03 pdb=" O LEU D 609 " -0.044 2.00e-02 2.50e+03 pdb=" N TRP D 610 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 533 " 0.025 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C PHE A 533 " -0.095 2.00e-02 2.50e+03 pdb=" O PHE A 533 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS A 534 " 0.034 2.00e-02 2.50e+03 ... (remaining 3543 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 367 2.68 - 3.23: 18024 3.23 - 3.79: 27037 3.79 - 4.34: 31120 4.34 - 4.90: 53219 Nonbonded interactions: 129767 Sorted by model distance: nonbonded pdb=" O MET B 818 " pdb=" CD1 PHE B 822 " model vdw 2.124 3.340 nonbonded pdb=" O MET D 818 " pdb=" CD1 PHE D 822 " model vdw 2.125 3.340 nonbonded pdb=" O SER B 617 " pdb=" OG SER B 617 " model vdw 2.232 3.040 nonbonded pdb=" O SER D 617 " pdb=" OG SER D 617 " model vdw 2.232 3.040 nonbonded pdb=" O THR C 35 " pdb=" N HIS C 38 " model vdw 2.283 3.120 ... (remaining 129762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 55.370 Find NCS groups from input model: 1.020 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.175 19522 Z= 0.481 Angle : 0.982 32.582 26914 Z= 0.640 Chirality : 0.068 1.031 3416 Planarity : 0.006 0.068 3546 Dihedral : 11.574 74.183 5290 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.80 % Favored : 95.07 % Rotamer: Outliers : 5.24 % Allowed : 6.27 % Favored : 88.48 % Cbeta Deviations : 1.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -2.47 (0.13), residues: 3144 helix: -0.41 (0.13), residues: 1312 sheet: -2.02 (0.22), residues: 432 loop : -2.74 (0.14), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 610 HIS 0.012 0.002 HIS C 780 PHE 0.058 0.003 PHE D 460 TYR 0.026 0.001 TYR C 692 ARG 0.006 0.000 ARG A 722 *********************** 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 371 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 315 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7155 (mtp) cc_final: 0.6735 (ttm) REVERT: A 641 MET cc_start: 0.8762 (tmt) cc_final: 0.8422 (tmt) REVERT: A 651 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8869 (tp) REVERT: A 693 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7522 (t80) REVERT: B 391 TRP cc_start: 0.6977 (OUTLIER) cc_final: 0.6223 (t60) REVERT: B 554 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.5556 (m-10) REVERT: B 630 ILE cc_start: 0.8291 (mm) cc_final: 0.8026 (mt) REVERT: B 643 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9092 (tt) REVERT: C 501 MET cc_start: 0.7269 (mtp) cc_final: 0.6747 (ttm) REVERT: C 536 GLN cc_start: 0.7924 (pp30) cc_final: 0.7711 (pp30) REVERT: C 641 MET cc_start: 0.8838 (tmt) cc_final: 0.8477 (tmt) REVERT: C 651 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8927 (tp) REVERT: C 693 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7444 (t80) REVERT: D 391 TRP cc_start: 0.7153 (OUTLIER) cc_final: 0.5901 (t60) REVERT: D 630 ILE cc_start: 0.8324 (mm) cc_final: 0.8051 (mt) REVERT: D 643 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9040 (tt) outliers start: 56 outliers final: 37 residues processed: 365 average time/residue: 0.2280 time to fit residues: 139.1683 Evaluate side-chains 285 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 239 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 532 PRO Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 608 TRP Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 532 PRO Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 692 TYR Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 507 TYR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 643 LEU 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: 6.9990 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 50.0000 chunk 160 optimal weight: 50.0000 chunk 127 optimal weight: 0.7980 chunk 246 optimal weight: 50.0000 chunk 95 optimal weight: 30.0000 chunk 149 optimal weight: 0.9980 chunk 183 optimal weight: 30.0000 chunk 285 optimal weight: 1.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 477 HIS A 771 GLN C 477 HIS C 771 GLN D 694 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19522 Z= 0.448 Angle : 0.673 8.287 26914 Z= 0.372 Chirality : 0.048 0.253 3416 Planarity : 0.005 0.077 3546 Dihedral : 6.786 59.408 3327 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.08 % Favored : 93.73 % Rotamer: Outliers : 7.87 % Allowed : 16.57 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 3144 helix: 0.76 (0.14), residues: 1352 sheet: -1.49 (0.26), residues: 322 loop : -2.38 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 607 HIS 0.006 0.002 HIS C 780 PHE 0.039 0.003 PHE C 533 TYR 0.033 0.002 TYR D 479 ARG 0.004 0.001 ARG A 763 *********************** 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 318 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 234 time to evaluate : 2.144 Fit side-chains REVERT: A 565 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7480 (tp) REVERT: B 391 TRP cc_start: 0.6905 (OUTLIER) cc_final: 0.6087 (t60) REVERT: B 554 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.6063 (m-10) REVERT: B 671 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.6747 (m-10) REVERT: D 391 TRP cc_start: 0.7029 (OUTLIER) cc_final: 0.5765 (t60) REVERT: D 554 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6528 (m-10) REVERT: D 671 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.6782 (m-10) outliers start: 84 outliers final: 55 residues processed: 300 average time/residue: 0.2135 time to fit residues: 111.4607 Evaluate side-chains 276 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 214 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 835 ILE Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 40.0000 chunk 88 optimal weight: 40.0000 chunk 237 optimal weight: 20.0000 chunk 194 optimal weight: 0.4980 chunk 78 optimal weight: 9.9990 chunk 285 optimal weight: 0.9990 chunk 308 optimal weight: 0.7980 chunk 254 optimal weight: 50.0000 chunk 283 optimal weight: 0.6980 chunk 97 optimal weight: 50.0000 chunk 229 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 19522 Z= 0.167 Angle : 0.500 7.187 26914 Z= 0.273 Chirality : 0.043 0.180 3416 Planarity : 0.003 0.076 3546 Dihedral : 5.528 59.093 3274 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 5.15 % Allowed : 22.28 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.68 (0.15), residues: 3144 helix: 1.35 (0.15), residues: 1360 sheet: -1.37 (0.24), residues: 426 loop : -2.09 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 636 HIS 0.004 0.001 HIS A 404 PHE 0.046 0.001 PHE C 654 TYR 0.018 0.001 TYR D 705 ARG 0.001 0.000 ARG D 540 *********************** 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 284 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 229 time to evaluate : 2.171 Fit side-chains REVERT: B 554 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.5969 (m-10) REVERT: B 643 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8154 (mt) REVERT: B 666 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8682 (pp) REVERT: B 834 ILE cc_start: 0.8706 (pt) cc_final: 0.8396 (mt) REVERT: D 554 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6485 (m-10) REVERT: D 666 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8732 (pp) outliers start: 55 outliers final: 34 residues processed: 276 average time/residue: 0.2114 time to fit residues: 102.0132 Evaluate side-chains 262 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 223 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 31 optimal weight: 30.0000 chunk 136 optimal weight: 0.7980 chunk 191 optimal weight: 40.0000 chunk 286 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 271 optimal weight: 0.6980 chunk 81 optimal weight: 50.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19522 Z= 0.272 Angle : 0.550 7.920 26914 Z= 0.299 Chirality : 0.044 0.189 3416 Planarity : 0.004 0.068 3546 Dihedral : 5.365 57.989 3270 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 7.21 % Allowed : 22.57 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.45 (0.15), residues: 3144 helix: 1.58 (0.15), residues: 1338 sheet: -1.56 (0.25), residues: 360 loop : -1.83 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 636 HIS 0.006 0.001 HIS C 477 PHE 0.044 0.002 PHE A 654 TYR 0.030 0.002 TYR B 479 ARG 0.003 0.000 ARG C 763 *********************** 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 302 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 225 time to evaluate : 2.150 Fit side-chains REVERT: A 565 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7364 (tp) REVERT: A 615 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8702 (mt) REVERT: B 554 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6208 (m-10) REVERT: B 671 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.6762 (m-10) REVERT: B 834 ILE cc_start: 0.8735 (pt) cc_final: 0.8444 (mt) REVERT: C 501 MET cc_start: 0.7847 (mtp) cc_final: 0.7565 (ttm) REVERT: C 511 ASP cc_start: 0.8146 (m-30) cc_final: 0.7866 (m-30) REVERT: C 565 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7464 (tp) REVERT: C 615 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8675 (mt) REVERT: D 554 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.6426 (m-10) REVERT: D 671 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.6705 (m-10) REVERT: D 834 ILE cc_start: 0.8652 (pt) cc_final: 0.8359 (mt) outliers start: 77 outliers final: 50 residues processed: 283 average time/residue: 0.2123 time to fit residues: 104.5645 Evaluate side-chains 276 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 218 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU 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: 7.9990 chunk 4 optimal weight: 50.0000 chunk 225 optimal weight: 3.9990 chunk 125 optimal weight: 0.0370 chunk 259 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 0 optimal weight: 100.0000 chunk 154 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19522 Z= 0.335 Angle : 0.583 7.840 26914 Z= 0.316 Chirality : 0.045 0.169 3416 Planarity : 0.004 0.061 3546 Dihedral : 5.432 58.071 3268 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.17 % Favored : 93.77 % Rotamer: Outliers : 8.99 % Allowed : 23.22 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.42 (0.15), residues: 3144 helix: 1.60 (0.15), residues: 1338 sheet: -1.03 (0.27), residues: 326 loop : -1.98 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 636 HIS 0.006 0.001 HIS A 477 PHE 0.032 0.002 PHE C 533 TYR 0.034 0.002 TYR C 703 ARG 0.005 0.000 ARG C 763 *********************** 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 311 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 215 time to evaluate : 2.144 Fit side-chains REVERT: A 565 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7428 (tp) REVERT: A 615 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8776 (mt) REVERT: A 709 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7551 (p90) REVERT: B 391 TRP cc_start: 0.6853 (OUTLIER) cc_final: 0.6027 (t60) REVERT: B 554 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6324 (m-10) REVERT: B 671 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.6745 (m-10) REVERT: B 834 ILE cc_start: 0.8696 (pt) cc_final: 0.8461 (mt) REVERT: C 565 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7474 (tp) REVERT: C 615 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8763 (mt) REVERT: C 709 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.7573 (p90) REVERT: D 391 TRP cc_start: 0.7039 (OUTLIER) cc_final: 0.5851 (t60) REVERT: D 464 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8568 (tp) REVERT: D 468 ILE cc_start: 0.8617 (mt) cc_final: 0.8377 (mt) REVERT: D 554 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6410 (m-10) REVERT: D 671 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.6836 (m-10) outliers start: 96 outliers final: 58 residues processed: 296 average time/residue: 0.2190 time to fit residues: 112.0470 Evaluate side-chains 277 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 206 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 10.0000 chunk 273 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 178 optimal weight: 0.0000 chunk 74 optimal weight: 0.9990 chunk 303 optimal weight: 0.3980 chunk 252 optimal weight: 20.0000 chunk 140 optimal weight: 0.2980 chunk 25 optimal weight: 10.0000 chunk 100 optimal weight: 50.0000 chunk 159 optimal weight: 50.0000 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19522 Z= 0.141 Angle : 0.484 9.073 26914 Z= 0.256 Chirality : 0.042 0.173 3416 Planarity : 0.003 0.055 3546 Dihedral : 4.824 59.170 3266 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.53 % Rotamer: Outliers : 7.02 % Allowed : 25.37 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.15 (0.16), residues: 3144 helix: 1.82 (0.15), residues: 1352 sheet: -1.47 (0.26), residues: 342 loop : -1.69 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 636 HIS 0.004 0.001 HIS A 404 PHE 0.015 0.001 PHE A 609 TYR 0.016 0.001 TYR D 479 ARG 0.002 0.000 ARG C 523 *********************** 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 294 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 219 time to evaluate : 2.272 Fit side-chains REVERT: B 554 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6067 (m-10) REVERT: C 709 HIS cc_start: 0.8240 (OUTLIER) cc_final: 0.7700 (p90) REVERT: D 434 VAL cc_start: 0.8591 (m) cc_final: 0.8344 (m) REVERT: D 554 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6373 (m-10) outliers start: 75 outliers final: 51 residues processed: 280 average time/residue: 0.2218 time to fit residues: 107.9826 Evaluate side-chains 265 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 211 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 1.9990 chunk 34 optimal weight: 40.0000 chunk 173 optimal weight: 30.0000 chunk 221 optimal weight: 0.5980 chunk 171 optimal weight: 7.9990 chunk 255 optimal weight: 50.0000 chunk 169 optimal weight: 0.9980 chunk 302 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 184 optimal weight: 50.0000 chunk 139 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19522 Z= 0.271 Angle : 0.550 9.784 26914 Z= 0.291 Chirality : 0.044 0.227 3416 Planarity : 0.003 0.051 3546 Dihedral : 4.761 59.279 3262 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % Rotamer: Outliers : 7.77 % Allowed : 24.53 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 3144 helix: 1.90 (0.15), residues: 1336 sheet: -1.16 (0.27), residues: 364 loop : -1.70 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 636 HIS 0.005 0.001 HIS A 477 PHE 0.030 0.002 PHE C 533 TYR 0.028 0.001 TYR B 479 ARG 0.003 0.000 ARG A 763 *********************** 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: 83 poor density : 204 time to evaluate : 2.151 Fit side-chains REVERT: B 391 TRP cc_start: 0.6852 (OUTLIER) cc_final: 0.6028 (t60) REVERT: B 554 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6164 (m-10) REVERT: B 671 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.6749 (m-10) REVERT: C 709 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7728 (p90) REVERT: D 554 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6418 (m-10) REVERT: D 671 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.6717 (m-10) outliers start: 83 outliers final: 58 residues processed: 274 average time/residue: 0.2234 time to fit residues: 106.0949 Evaluate side-chains 268 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 204 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 192 optimal weight: 0.0170 chunk 206 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19522 Z= 0.219 Angle : 0.523 9.055 26914 Z= 0.275 Chirality : 0.043 0.264 3416 Planarity : 0.003 0.046 3546 Dihedral : 4.613 57.085 3262 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 6.18 % Allowed : 26.40 % Favored : 67.42 % 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: -0.01 (0.16), residues: 3144 helix: 1.92 (0.15), residues: 1342 sheet: -1.28 (0.26), residues: 388 loop : -1.59 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 636 HIS 0.004 0.001 HIS C 404 PHE 0.024 0.002 PHE A 533 TYR 0.023 0.001 TYR B 479 ARG 0.001 0.000 ARG D 693 *********************** 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 270 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 204 time to evaluate : 1.993 Fit side-chains REVERT: B 391 TRP cc_start: 0.6857 (OUTLIER) cc_final: 0.5953 (t60) REVERT: B 554 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6225 (m-10) REVERT: B 671 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.6831 (m-10) REVERT: D 391 TRP cc_start: 0.7030 (OUTLIER) cc_final: 0.5829 (t60) REVERT: D 554 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6380 (m-10) REVERT: D 671 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.6799 (m-10) outliers start: 66 outliers final: 56 residues processed: 261 average time/residue: 0.2241 time to fit residues: 100.8407 Evaluate side-chains 263 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 201 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 264 optimal weight: 30.0000 chunk 282 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 254 optimal weight: 50.0000 chunk 266 optimal weight: 40.0000 chunk 281 optimal weight: 0.3980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19522 Z= 0.201 Angle : 0.518 9.504 26914 Z= 0.270 Chirality : 0.043 0.316 3416 Planarity : 0.003 0.084 3546 Dihedral : 4.420 58.253 3258 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.24 % Rotamer: Outliers : 6.37 % Allowed : 26.31 % Favored : 67.32 % 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: 0.08 (0.16), residues: 3144 helix: 1.97 (0.15), residues: 1344 sheet: -1.15 (0.27), residues: 374 loop : -1.56 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 636 HIS 0.004 0.001 HIS C 404 PHE 0.022 0.002 PHE C 533 TYR 0.023 0.001 TYR B 479 ARG 0.002 0.000 ARG A 763 *********************** 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 268 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 200 time to evaluate : 1.866 Fit side-chains REVERT: B 391 TRP cc_start: 0.6857 (OUTLIER) cc_final: 0.5942 (t60) REVERT: B 554 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6307 (m-10) REVERT: B 671 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.6742 (m-10) REVERT: D 554 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6463 (m-10) REVERT: D 671 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.6736 (m-10) outliers start: 68 outliers final: 54 residues processed: 259 average time/residue: 0.2176 time to fit residues: 97.9928 Evaluate side-chains 254 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 195 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 0.0170 chunk 298 optimal weight: 0.9990 chunk 182 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 312 optimal weight: 0.7980 chunk 287 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 25 optimal weight: 30.0000 chunk 192 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19522 Z= 0.172 Angle : 0.502 11.552 26914 Z= 0.259 Chirality : 0.043 0.288 3416 Planarity : 0.003 0.079 3546 Dihedral : 4.263 59.697 3256 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.09 % Allowed : 26.78 % Favored : 67.13 % 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: 1.97 (0.15), residues: 1358 sheet: -1.05 (0.27), residues: 374 loop : -1.42 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 636 HIS 0.004 0.001 HIS A 404 PHE 0.019 0.001 PHE A 654 TYR 0.019 0.001 TYR B 479 ARG 0.001 0.000 ARG A 763 ********************** 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 262 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 197 time to evaluate : 2.289 Fit side-chains REVERT: B 391 TRP cc_start: 0.6897 (OUTLIER) cc_final: 0.6000 (t60) REVERT: B 554 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6225 (m-10) REVERT: B 671 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.6855 (m-10) REVERT: D 391 TRP cc_start: 0.7026 (OUTLIER) cc_final: 0.5909 (t60) REVERT: D 554 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.6468 (m-10) REVERT: D 671 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.6795 (m-10) outliers start: 65 outliers final: 55 residues processed: 255 average time/residue: 0.2242 time to fit residues: 99.0473 Evaluate side-chains 256 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 195 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 76 optimal weight: 0.4980 chunk 229 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 0.0170 chunk 249 optimal weight: 2.9990 chunk 104 optimal weight: 50.0000 chunk 256 optimal weight: 50.0000 chunk 31 optimal weight: 50.0000 chunk 45 optimal weight: 8.9990 overall best weight: 2.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.197116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.170989 restraints weight = 30670.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.167313 restraints weight = 45535.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.164291 restraints weight = 49267.339| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19522 Z= 0.324 Angle : 0.590 11.089 26914 Z= 0.310 Chirality : 0.045 0.298 3416 Planarity : 0.003 0.076 3546 Dihedral : 4.536 59.131 3254 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 6.37 % Allowed : 27.06 % Favored : 66.57 % 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: 0.10 (0.16), residues: 3144 helix: 1.85 (0.15), residues: 1360 sheet: -0.79 (0.29), residues: 324 loop : -1.52 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 636 HIS 0.007 0.001 HIS C 477 PHE 0.034 0.002 PHE C 533 TYR 0.034 0.002 TYR B 479 ARG 0.004 0.000 ARG A 763 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3621.13 seconds wall clock time: 64 minutes 25.70 seconds (3865.70 seconds total)