Starting phenix.real_space_refine on Sat Jul 20 17:58:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/07_2024/8t6j_41069.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/07_2024/8t6j_41069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/07_2024/8t6j_41069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/07_2024/8t6j_41069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/07_2024/8t6j_41069.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/07_2024/8t6j_41069.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 7473 2.51 5 N 1940 2.21 5 O 2127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B ASP 433": "OD1" <-> "OD2" Residue "B TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 498": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11652 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5803 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 150 Chain: "A" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5793 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 156 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'YKU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'YKU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.61, per 1000 atoms: 0.65 Number of scatterers: 11652 At special positions: 0 Unit cell: (123.555, 82.6537, 188.314, 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 112 16.00 O 2127 8.00 N 1940 7.00 C 7473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " 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: 4.36 Conformation dependent library (CDL) restraints added in 2.1 seconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 18 sheets defined 51.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.670A pdb=" N VAL B 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.500A pdb=" N ALA B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.896A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.889A pdb=" N SER B 180 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 197 through 209 removed outlier: 3.588A pdb=" N VAL B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.975A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.666A pdb=" N ARG B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 removed outlier: 4.378A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.807A pdb=" N ASN B 349 " --> pdb=" O PRO B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.923A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 443 removed outlier: 3.929A pdb=" N LEU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.833A pdb=" N VAL B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 500' Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 577 through 604 removed outlier: 3.694A pdb=" N ILE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 614 through 630 Processing helix chain 'B' and resid 631 through 637 removed outlier: 3.723A pdb=" N ALA B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 673 removed outlier: 4.223A pdb=" N CYS B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR B 645 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 651 " --> pdb=" O GLN B 647 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 4.272A pdb=" N SER B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 715 removed outlier: 3.535A pdb=" N GLN B 693 " --> pdb=" O SER B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 761 Proline residue: B 743 - end of helix removed outlier: 4.097A pdb=" N LEU B 749 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B 750 " --> pdb=" O TYR B 746 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 793 removed outlier: 3.594A pdb=" N ASN B 769 " --> pdb=" O PRO B 765 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET B 778 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR B 780 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 781 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B 789 " --> pdb=" O TRP B 785 " (cutoff:3.500A) Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 797 through 816 removed outlier: 3.931A pdb=" N VAL B 806 " --> pdb=" O MET B 802 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 807 " --> pdb=" O CYS B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 827 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.742A pdb=" N VAL A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.685A pdb=" N ILE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.883A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.893A pdb=" N SER A 180 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'A' and resid 197 through 209 removed outlier: 3.588A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.729A pdb=" N SER A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.655A pdb=" N ARG A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.558A pdb=" N VAL A 313 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 4.388A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.790A pdb=" N ASN A 349 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.930A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 4.072A pdb=" N LYS A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 443 removed outlier: 3.895A pdb=" N LEU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.859A pdb=" N VAL A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 500' Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 577 through 604 removed outlier: 3.697A pdb=" N ILE A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 614 through 630 Processing helix chain 'A' and resid 631 through 637 removed outlier: 3.662A pdb=" N ALA A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 673 removed outlier: 4.241A pdb=" N CYS A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 4.298A pdb=" N SER A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 715 removed outlier: 3.523A pdb=" N GLN A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 761 Proline residue: A 743 - end of helix removed outlier: 4.044A pdb=" N LEU A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 750 " --> pdb=" O TYR A 746 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 793 removed outlier: 3.582A pdb=" N ASN A 769 " --> pdb=" O PRO A 765 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 789 " --> pdb=" O TRP A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 797 through 816 removed outlier: 3.927A pdb=" N VAL A 806 " --> pdb=" O MET A 802 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 807 " --> pdb=" O CYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 827 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.262A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 213 through 216 removed outlier: 7.768A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.291A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 327 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 468 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 485 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AA5, first strand: chain 'B' and resid 471 through 475 removed outlier: 3.570A pdb=" N LYS B 472 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 480 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 520 through 522 Processing sheet with id=AA7, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AA8, first strand: chain 'B' and resid 556 through 558 Processing sheet with id=AA9, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.609A pdb=" N ASP B 722 " --> pdb=" O TYR B 730 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.258A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 213 through 216 removed outlier: 7.759A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 274 through 276 removed outlier: 3.714A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 326 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 472 " --> pdb=" O ASP A 480 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A 480 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 274 through 276 removed outlier: 3.714A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 326 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 468 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 485 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AB6, first strand: chain 'A' and resid 520 through 522 Processing sheet with id=AB7, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AB8, first strand: chain 'A' and resid 556 through 558 Processing sheet with id=AB9, first strand: chain 'A' and resid 719 through 722 removed outlier: 3.606A pdb=" N ASP A 722 " --> pdb=" O TYR A 730 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1527 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: 3.90 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1887 1.27 - 1.41: 3001 1.41 - 1.55: 6857 1.55 - 1.68: 11 1.68 - 1.82: 162 Bond restraints: 11918 Sorted by residual: bond pdb=" C19 YKU B 901 " pdb=" C21 YKU B 901 " ideal model delta sigma weight residual 1.429 1.527 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C19 YKU A 901 " pdb=" C21 YKU A 901 " ideal model delta sigma weight residual 1.429 1.526 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C13 YKU A 901 " pdb=" N12 YKU A 901 " ideal model delta sigma weight residual 1.359 1.454 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C13 YKU B 901 " pdb=" N12 YKU B 901 " ideal model delta sigma weight residual 1.359 1.453 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C04 YKU B 901 " pdb=" C07 YKU B 901 " ideal model delta sigma weight residual 1.465 1.528 -0.063 2.00e-02 2.50e+03 9.87e+00 ... (remaining 11913 not shown) Histogram of bond angle deviations from ideal: 98.74 - 114.85: 7432 114.85 - 130.96: 8725 130.96 - 147.07: 51 147.07 - 163.18: 0 163.18 - 179.29: 2 Bond angle restraints: 16210 Sorted by residual: angle pdb=" CB LYS B 51 " pdb=" CG LYS B 51 " pdb=" CD LYS B 51 " ideal model delta sigma weight residual 111.30 117.90 -6.60 2.30e+00 1.89e-01 8.23e+00 angle pdb=" CA LEU B 295 " pdb=" CB LEU B 295 " pdb=" CG LEU B 295 " ideal model delta sigma weight residual 116.30 126.29 -9.99 3.50e+00 8.16e-02 8.15e+00 angle pdb=" CB ARG B 114 " pdb=" CG ARG B 114 " pdb=" CD ARG B 114 " ideal model delta sigma weight residual 111.30 104.76 6.54 2.30e+00 1.89e-01 8.09e+00 angle pdb=" CB MET A 474 " pdb=" CG MET A 474 " pdb=" SD MET A 474 " ideal model delta sigma weight residual 112.70 121.19 -8.49 3.00e+00 1.11e-01 8.01e+00 angle pdb=" CB LYS A 51 " pdb=" CG LYS A 51 " pdb=" CD LYS A 51 " ideal model delta sigma weight residual 111.30 117.26 -5.96 2.30e+00 1.89e-01 6.71e+00 ... (remaining 16205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6401 17.97 - 35.94: 559 35.94 - 53.91: 105 53.91 - 71.88: 20 71.88 - 89.85: 3 Dihedral angle restraints: 7088 sinusoidal: 2630 harmonic: 4458 Sorted by residual: dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual 93.00 135.61 -42.61 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CB CYS B 419 " pdb=" SG CYS B 419 " pdb=" SG CYS B 426 " pdb=" CB CYS B 426 " ideal model delta sinusoidal sigma weight residual -86.00 -44.07 -41.93 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CB CYS B 511 " pdb=" SG CYS B 511 " pdb=" SG CYS B 531 " pdb=" CB CYS B 531 " ideal model delta sinusoidal sigma weight residual 93.00 134.68 -41.68 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 7085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1000 0.027 - 0.054: 531 0.054 - 0.082: 203 0.082 - 0.109: 84 0.109 - 0.136: 34 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA ILE B 568 " pdb=" N ILE B 568 " pdb=" C ILE B 568 " pdb=" CB ILE B 568 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE A 568 " pdb=" N ILE A 568 " pdb=" C ILE A 568 " pdb=" CB ILE A 568 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA VAL B 217 " pdb=" N VAL B 217 " pdb=" C VAL B 217 " pdb=" CB VAL B 217 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1849 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 789 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 790 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 790 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 790 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 789 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO B 790 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 790 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 790 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 764 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 765 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 765 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 765 " 0.017 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 791 2.74 - 3.28: 11449 3.28 - 3.82: 18007 3.82 - 4.36: 19638 4.36 - 4.90: 36335 Nonbonded interactions: 86220 Sorted by model distance: nonbonded pdb=" OG SER B 152 " pdb=" OG SER B 176 " model vdw 2.196 2.440 nonbonded pdb=" OG SER A 152 " pdb=" OG SER A 176 " model vdw 2.221 2.440 nonbonded pdb=" O ARG B 435 " pdb=" NH1 ARG B 435 " model vdw 2.228 2.520 nonbonded pdb=" O ARG A 435 " pdb=" NH1 ARG A 435 " model vdw 2.229 2.520 nonbonded pdb=" O GLY A 253 " pdb=" OG SER A 256 " model vdw 2.274 2.440 ... (remaining 86215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 515 or (resid 516 through 517 and (name N or na \ me CA or name C or name O or name CB )) or resid 518 through 827 or resid 901)) selection = (chain 'B' and (resid 26 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 552 or (resid 553 and (name N o \ r name CA or name C or name O or name CB )) or resid 554 through 559 or (resid 5 \ 60 through 561 and (name N or name CA or name C or name O or name CB )) or resid \ 562 through 827 or resid 901)) } 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.260 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.003 0.098 11918 Z= 0.238 Angle : 0.563 9.992 16210 Z= 0.289 Chirality : 0.041 0.136 1852 Planarity : 0.003 0.036 2058 Dihedral : 13.787 89.854 4176 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.00 (0.23), residues: 1522 helix: 1.52 (0.21), residues: 648 sheet: -1.22 (0.42), residues: 172 loop : -1.14 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.004 0.001 HIS B 30 PHE 0.013 0.001 PHE B 544 TYR 0.010 0.001 TYR B 223 ARG 0.013 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: B 657 MET cc_start: 0.6699 (ptm) cc_final: 0.6420 (ptt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2096 time to fit residues: 48.4397 Evaluate side-chains 124 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 11918 Z= 0.493 Angle : 0.688 7.087 16210 Z= 0.362 Chirality : 0.047 0.155 1852 Planarity : 0.005 0.062 2058 Dihedral : 5.090 36.213 1654 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.73 % Allowed : 10.65 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.37 (0.22), residues: 1522 helix: 1.21 (0.21), residues: 664 sheet: -1.36 (0.40), residues: 178 loop : -1.41 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 487 HIS 0.005 0.002 HIS B 30 PHE 0.018 0.002 PHE A 712 TYR 0.019 0.002 TYR B 340 ARG 0.008 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 GLU cc_start: 0.6375 (mt-10) cc_final: 0.6146 (mt-10) outliers start: 21 outliers final: 16 residues processed: 142 average time/residue: 0.2277 time to fit residues: 47.5150 Evaluate side-chains 140 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 GLN B 747 ASN A 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11918 Z= 0.180 Angle : 0.514 5.946 16210 Z= 0.269 Chirality : 0.041 0.147 1852 Planarity : 0.003 0.032 2058 Dihedral : 4.507 30.320 1654 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.31 % Allowed : 11.64 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.00 (0.23), residues: 1522 helix: 1.64 (0.21), residues: 654 sheet: -1.42 (0.40), residues: 184 loop : -1.22 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.003 0.001 HIS A 218 PHE 0.019 0.001 PHE A 712 TYR 0.013 0.001 TYR B 249 ARG 0.005 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 688 MET cc_start: 0.6916 (mmt) cc_final: 0.6616 (mmt) REVERT: A 416 MET cc_start: 0.8013 (ttp) cc_final: 0.7794 (ttp) outliers start: 28 outliers final: 16 residues processed: 149 average time/residue: 0.2315 time to fit residues: 50.7224 Evaluate side-chains 144 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 0.0060 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 0.0980 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 GLN A 571 GLN A 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11918 Z= 0.230 Angle : 0.525 6.114 16210 Z= 0.273 Chirality : 0.042 0.148 1852 Planarity : 0.004 0.031 2058 Dihedral : 4.384 26.394 1654 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.56 % Allowed : 13.96 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.03 (0.22), residues: 1522 helix: 1.68 (0.21), residues: 654 sheet: -1.48 (0.40), residues: 184 loop : -1.20 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.004 0.001 HIS A 218 PHE 0.025 0.001 PHE A 712 TYR 0.019 0.001 TYR A 340 ARG 0.008 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.7996 (ttp) cc_final: 0.7770 (ttp) outliers start: 31 outliers final: 21 residues processed: 149 average time/residue: 0.2151 time to fit residues: 47.9925 Evaluate side-chains 149 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11918 Z= 0.373 Angle : 0.605 6.383 16210 Z= 0.317 Chirality : 0.045 0.151 1852 Planarity : 0.004 0.048 2058 Dihedral : 4.620 23.544 1654 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.73 % Allowed : 15.52 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.23 (0.22), residues: 1522 helix: 1.49 (0.21), residues: 656 sheet: -1.70 (0.39), residues: 184 loop : -1.35 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 487 HIS 0.005 0.001 HIS A 218 PHE 0.027 0.002 PHE A 712 TYR 0.021 0.002 TYR B 340 ARG 0.008 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8062 (mmp) cc_final: 0.7807 (mmp) REVERT: B 601 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.6627 (t80) REVERT: B 657 MET cc_start: 0.7355 (ptm) cc_final: 0.6955 (ptt) REVERT: A 601 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.6609 (t80) outliers start: 33 outliers final: 26 residues processed: 156 average time/residue: 0.2206 time to fit residues: 50.3049 Evaluate side-chains 159 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 GLN A 571 GLN A 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11918 Z= 0.214 Angle : 0.536 7.915 16210 Z= 0.278 Chirality : 0.042 0.154 1852 Planarity : 0.004 0.031 2058 Dihedral : 4.373 21.930 1654 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.81 % Allowed : 16.68 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.06 (0.22), residues: 1522 helix: 1.63 (0.21), residues: 654 sheet: -1.63 (0.39), residues: 184 loop : -1.23 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.004 0.001 HIS A 218 PHE 0.028 0.001 PHE A 712 TYR 0.020 0.001 TYR B 340 ARG 0.007 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8047 (mmp) cc_final: 0.7795 (mmp) REVERT: B 494 MET cc_start: 0.9400 (ttt) cc_final: 0.9166 (ttt) REVERT: B 601 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.6580 (t80) REVERT: A 79 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7628 (tt) REVERT: A 474 MET cc_start: 0.7981 (mmp) cc_final: 0.7768 (mmm) REVERT: A 494 MET cc_start: 0.9392 (ttt) cc_final: 0.9160 (ttt) REVERT: A 588 CYS cc_start: 0.6500 (m) cc_final: 0.6287 (m) REVERT: A 601 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6573 (t80) outliers start: 34 outliers final: 26 residues processed: 160 average time/residue: 0.2214 time to fit residues: 52.3741 Evaluate side-chains 160 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11918 Z= 0.202 Angle : 0.531 11.488 16210 Z= 0.273 Chirality : 0.042 0.153 1852 Planarity : 0.003 0.031 2058 Dihedral : 4.255 20.442 1654 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.22 % Allowed : 17.34 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.03 (0.22), residues: 1522 helix: 1.59 (0.21), residues: 668 sheet: -1.57 (0.39), residues: 184 loop : -1.23 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 575 HIS 0.003 0.001 HIS A 30 PHE 0.028 0.001 PHE A 712 TYR 0.018 0.001 TYR A 629 ARG 0.007 0.000 ARG B 524 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 134 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8029 (mmp) cc_final: 0.7769 (mmp) REVERT: B 494 MET cc_start: 0.9392 (ttt) cc_final: 0.9147 (ttt) REVERT: B 601 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6570 (t80) REVERT: A 79 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7766 (tt) REVERT: A 494 MET cc_start: 0.9396 (ttt) cc_final: 0.9156 (ttt) REVERT: A 588 CYS cc_start: 0.6571 (m) cc_final: 0.6356 (m) REVERT: A 601 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6573 (t80) outliers start: 39 outliers final: 30 residues processed: 164 average time/residue: 0.2106 time to fit residues: 51.6983 Evaluate side-chains 166 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 GLN A 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11918 Z= 0.166 Angle : 0.516 12.388 16210 Z= 0.262 Chirality : 0.041 0.150 1852 Planarity : 0.003 0.032 2058 Dihedral : 4.051 18.710 1654 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.81 % Allowed : 17.59 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 (0.22), residues: 1522 helix: 1.69 (0.21), residues: 668 sheet: -1.34 (0.39), residues: 180 loop : -1.21 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 575 HIS 0.003 0.001 HIS A 30 PHE 0.029 0.001 PHE A 712 TYR 0.017 0.001 TYR A 629 ARG 0.007 0.000 ARG B 524 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8035 (mmp) cc_final: 0.7791 (mmp) REVERT: B 494 MET cc_start: 0.9398 (ttt) cc_final: 0.9160 (ttt) REVERT: B 601 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6528 (t80) REVERT: B 688 MET cc_start: 0.6870 (mmt) cc_final: 0.6524 (mmt) REVERT: A 79 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7779 (tt) REVERT: A 474 MET cc_start: 0.8356 (mmm) cc_final: 0.8145 (mmp) REVERT: A 494 MET cc_start: 0.9414 (ttt) cc_final: 0.9165 (ttt) REVERT: A 588 CYS cc_start: 0.6490 (m) cc_final: 0.6278 (m) REVERT: A 601 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6492 (t80) outliers start: 34 outliers final: 29 residues processed: 159 average time/residue: 0.1955 time to fit residues: 47.4640 Evaluate side-chains 162 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 747 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 129 optimal weight: 0.0030 chunk 89 optimal weight: 0.0270 chunk 144 optimal weight: 3.9990 overall best weight: 0.7052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11918 Z= 0.166 Angle : 0.525 13.399 16210 Z= 0.263 Chirality : 0.041 0.149 1852 Planarity : 0.003 0.031 2058 Dihedral : 3.983 20.309 1654 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.89 % Allowed : 17.75 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.14 (0.22), residues: 1522 helix: 1.70 (0.21), residues: 668 sheet: -1.27 (0.39), residues: 180 loop : -1.18 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 575 HIS 0.003 0.001 HIS B 30 PHE 0.028 0.001 PHE A 712 TYR 0.017 0.001 TYR A 629 ARG 0.007 0.000 ARG B 524 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8027 (mmp) cc_final: 0.7771 (mmp) REVERT: B 494 MET cc_start: 0.9405 (ttt) cc_final: 0.9159 (ttt) REVERT: B 601 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6512 (t80) REVERT: B 688 MET cc_start: 0.6855 (mmt) cc_final: 0.6515 (mmt) REVERT: A 79 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 494 MET cc_start: 0.9414 (ttt) cc_final: 0.9167 (ttt) REVERT: A 588 CYS cc_start: 0.6496 (m) cc_final: 0.6282 (m) REVERT: A 601 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6493 (t80) outliers start: 35 outliers final: 30 residues processed: 156 average time/residue: 0.2032 time to fit residues: 48.1829 Evaluate side-chains 160 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 747 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11918 Z= 0.264 Angle : 0.567 13.490 16210 Z= 0.289 Chirality : 0.043 0.149 1852 Planarity : 0.004 0.035 2058 Dihedral : 4.151 19.743 1654 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.73 % Allowed : 18.17 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.03 (0.22), residues: 1522 helix: 1.59 (0.21), residues: 668 sheet: -1.52 (0.39), residues: 184 loop : -1.24 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 575 HIS 0.004 0.001 HIS B 30 PHE 0.028 0.002 PHE A 712 TYR 0.018 0.001 TYR A 629 ARG 0.007 0.000 ARG B 524 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8069 (mmp) cc_final: 0.7802 (mmp) REVERT: B 601 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.6561 (t80) REVERT: A 79 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7794 (tt) REVERT: A 588 CYS cc_start: 0.6605 (m) cc_final: 0.6379 (m) REVERT: A 601 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6548 (t80) outliers start: 33 outliers final: 29 residues processed: 156 average time/residue: 0.2117 time to fit residues: 50.0935 Evaluate side-chains 162 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 747 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 0.0270 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 GLN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.143508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.119578 restraints weight = 21984.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118481 restraints weight = 19549.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119436 restraints weight = 19808.427| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11918 Z= 0.171 Angle : 0.526 12.885 16210 Z= 0.266 Chirality : 0.041 0.150 1852 Planarity : 0.003 0.032 2058 Dihedral : 4.020 19.302 1654 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.06 % Allowed : 18.17 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 (0.22), residues: 1522 helix: 1.69 (0.21), residues: 668 sheet: -1.44 (0.39), residues: 184 loop : -1.17 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 575 HIS 0.003 0.001 HIS B 30 PHE 0.027 0.001 PHE A 712 TYR 0.019 0.001 TYR A 629 ARG 0.007 0.000 ARG B 524 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2197.71 seconds wall clock time: 40 minutes 42.77 seconds (2442.77 seconds total)