Starting phenix.real_space_refine on Thu Mar 14 23:41:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/03_2024/7wih_32530_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/03_2024/7wih_32530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/03_2024/7wih_32530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/03_2024/7wih_32530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/03_2024/7wih_32530_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wih_32530/03_2024/7wih_32530_updated.pdb" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 104 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 66 5.16 5 C 6320 2.51 5 N 1740 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 180": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 380": "OD1" <-> "OD2" Residue "B ASP 525": "OD1" <-> "OD2" Residue "B TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10002 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 4963 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 235} Link IDs: {'PTRANS': 28, 'TRANS': 712} Chain breaks: 4 Unresolved non-hydrogen bonds: 953 Unresolved non-hydrogen angles: 1211 Unresolved non-hydrogen dihedrals: 815 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 9, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 588 Chain: "B" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 4963 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 235} Link IDs: {'PTRANS': 28, 'TRANS': 712} Chain breaks: 4 Unresolved non-hydrogen bonds: 953 Unresolved non-hydrogen angles: 1211 Unresolved non-hydrogen dihedrals: 815 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 9, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 16, 'GLU:plan': 27, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 588 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'CWY': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'CWY': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.16, per 1000 atoms: 0.62 Number of scatterers: 10002 At special positions: 0 Unit cell: (104.442, 84.162, 179.478, 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 66 16.00 O 1876 8.00 N 1740 7.00 C 6320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 527 " distance=2.04 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 412 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 513 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 546 " distance=2.04 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A 730 " distance=2.04 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 373 " distance=2.02 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 513 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 546 " distance=2.04 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 641 " - pdb=" SG CYS B 730 " distance=2.04 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 209 " " NAG B 901 " - " ASN B 209 " Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 2.2 seconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2800 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 8 sheets defined 27.9% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 66 through 77 removed outlier: 4.559A pdb=" N ALA A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.858A pdb=" N LEU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 No H-bonds generated for 'chain 'A' and resid 152 through 155' Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 202 removed outlier: 4.266A pdb=" N ALA A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 257 through 260 No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 388 through 406 removed outlier: 3.859A pdb=" N MET A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE A 392 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 393 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 394 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 395 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 396 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA A 399 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A 402 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU A 404 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS A 405 " --> pdb=" O HIS A 402 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 406 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 579 through 585 Processing helix chain 'A' and resid 587 through 598 removed outlier: 4.227A pdb=" N THR A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR A 596 " --> pdb=" O CYS A 592 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 615 through 618 No H-bonds generated for 'chain 'A' and resid 615 through 618' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 641 through 653 removed outlier: 3.508A pdb=" N ARG A 645 " --> pdb=" O CYS A 641 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 665 Processing helix chain 'A' and resid 691 through 695 Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 734 through 749 removed outlier: 3.922A pdb=" N ASP A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU A 747 " --> pdb=" O TYR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 754 No H-bonds generated for 'chain 'A' and resid 751 through 754' Processing helix chain 'A' and resid 767 through 782 removed outlier: 4.886A pdb=" N GLY A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 778 " --> pdb=" O THR A 774 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N CYS A 779 " --> pdb=" O MET A 775 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 788 No H-bonds generated for 'chain 'A' and resid 786 through 788' Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.720A pdb=" N CYS A 804 " --> pdb=" O THR A 800 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 807 " --> pdb=" O MET A 803 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 808 " --> pdb=" O CYS A 804 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 809 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 810 " --> pdb=" O SER A 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 removed outlier: 4.560A pdb=" N ALA B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.858A pdb=" N LEU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 No H-bonds generated for 'chain 'B' and resid 152 through 155' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 195 through 202 removed outlier: 4.266A pdb=" N ALA B 200 " --> pdb=" O TYR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 234 No H-bonds generated for 'chain 'B' and resid 231 through 234' Processing helix chain 'B' and resid 257 through 260 No H-bonds generated for 'chain 'B' and resid 257 through 260' Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.859A pdb=" N MET B 391 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 392 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 393 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 394 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 395 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 396 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL B 397 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA B 399 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS B 402 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B 404 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 405 " --> pdb=" O HIS B 402 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 406 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 500 through 502 No H-bonds generated for 'chain 'B' and resid 500 through 502' Processing helix chain 'B' and resid 579 through 585 Processing helix chain 'B' and resid 587 through 598 removed outlier: 4.226A pdb=" N THR B 591 " --> pdb=" O GLY B 587 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR B 596 " --> pdb=" O CYS B 592 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 609 Processing helix chain 'B' and resid 615 through 618 No H-bonds generated for 'chain 'B' and resid 615 through 618' Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 641 through 653 removed outlier: 3.508A pdb=" N ARG B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 665 Processing helix chain 'B' and resid 691 through 695 Processing helix chain 'B' and resid 702 through 708 Processing helix chain 'B' and resid 734 through 749 removed outlier: 3.922A pdb=" N ASP B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 746 " --> pdb=" O THR B 742 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU B 747 " --> pdb=" O TYR B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 754 No H-bonds generated for 'chain 'B' and resid 751 through 754' Processing helix chain 'B' and resid 767 through 782 removed outlier: 4.887A pdb=" N GLY B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 778 " --> pdb=" O THR B 774 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 781 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 788 No H-bonds generated for 'chain 'B' and resid 786 through 788' Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.720A pdb=" N CYS B 804 " --> pdb=" O THR B 800 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 807 " --> pdb=" O MET B 803 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER B 808 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 809 " --> pdb=" O ILE B 805 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 810 " --> pdb=" O SER B 806 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 32 through 34 Processing sheet with id= B, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= C, first strand: chain 'A' and resid 214 through 216 removed outlier: 6.285A pdb=" N THR A 296 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 274 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 298 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 553 through 555 Processing sheet with id= E, first strand: chain 'B' and resid 32 through 34 Processing sheet with id= F, first strand: chain 'B' and resid 39 through 41 Processing sheet with id= G, first strand: chain 'B' and resid 214 through 216 removed outlier: 6.285A pdb=" N THR B 296 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU B 274 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 298 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 553 through 555 136 hydrogen bonds defined for protein. 378 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: 2.74 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1700 1.31 - 1.44: 2573 1.44 - 1.57: 5821 1.57 - 1.70: 4 1.70 - 1.83: 82 Bond restraints: 10180 Sorted by residual: bond pdb=" C CWY A 902 " pdb=" C7 CWY A 902 " ideal model delta sigma weight residual 1.537 1.315 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C CWY B 902 " pdb=" C7 CWY B 902 " ideal model delta sigma weight residual 1.537 1.316 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C1 CWY A 902 " pdb=" C3 CWY A 902 " ideal model delta sigma weight residual 1.533 1.355 0.178 2.00e-02 2.50e+03 7.94e+01 bond pdb=" C1 CWY B 902 " pdb=" C3 CWY B 902 " ideal model delta sigma weight residual 1.533 1.355 0.178 2.00e-02 2.50e+03 7.92e+01 bond pdb=" C8 CWY A 902 " pdb=" N1 CWY A 902 " ideal model delta sigma weight residual 1.342 1.461 -0.119 2.00e-02 2.50e+03 3.53e+01 ... (remaining 10175 not shown) Histogram of bond angle deviations from ideal: 59.62 - 76.68: 6 76.68 - 93.75: 0 93.75 - 110.81: 3448 110.81 - 127.88: 10434 127.88 - 144.94: 80 Bond angle restraints: 13968 Sorted by residual: angle pdb=" C4 CWY A 902 " pdb=" C6 CWY A 902 " pdb=" C7 CWY A 902 " ideal model delta sigma weight residual 116.66 144.94 -28.28 3.00e+00 1.11e-01 8.89e+01 angle pdb=" C4 CWY B 902 " pdb=" C6 CWY B 902 " pdb=" C7 CWY B 902 " ideal model delta sigma weight residual 116.66 144.92 -28.26 3.00e+00 1.11e-01 8.87e+01 angle pdb=" C TRP B 486 " pdb=" N ALA B 487 " pdb=" CA ALA B 487 " ideal model delta sigma weight residual 121.54 133.51 -11.97 1.91e+00 2.74e-01 3.93e+01 angle pdb=" C TRP A 486 " pdb=" N ALA A 487 " pdb=" CA ALA A 487 " ideal model delta sigma weight residual 121.54 133.49 -11.95 1.91e+00 2.74e-01 3.92e+01 angle pdb=" C VAL A 247 " pdb=" CA VAL A 247 " pdb=" CB VAL A 247 " ideal model delta sigma weight residual 110.70 116.28 -5.58 9.90e-01 1.02e+00 3.18e+01 ... (remaining 13963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5550 17.78 - 35.57: 459 35.57 - 53.35: 83 53.35 - 71.13: 28 71.13 - 88.91: 12 Dihedral angle restraints: 6132 sinusoidal: 1824 harmonic: 4308 Sorted by residual: dihedral pdb=" CB CYS A 240 " pdb=" SG CYS A 240 " pdb=" SG CYS A 527 " pdb=" CB CYS A 527 " ideal model delta sinusoidal sigma weight residual -86.00 -3.62 -82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS B 240 " pdb=" SG CYS B 240 " pdb=" SG CYS B 527 " pdb=" CB CYS B 527 " ideal model delta sinusoidal sigma weight residual -86.00 -3.63 -82.37 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS B 361 " pdb=" SG CYS B 361 " pdb=" SG CYS B 373 " pdb=" CB CYS B 373 " ideal model delta sinusoidal sigma weight residual -86.00 -143.20 57.20 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 6129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1698 0.165 - 0.329: 8 0.329 - 0.494: 2 0.494 - 0.659: 2 0.659 - 0.823: 2 Chirality restraints: 1712 Sorted by residual: chirality pdb=" C6 CWY A 902 " pdb=" C3 CWY A 902 " pdb=" C4 CWY A 902 " pdb=" C7 CWY A 902 " both_signs ideal model delta sigma weight residual True 2.64 1.81 0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C6 CWY B 902 " pdb=" C3 CWY B 902 " pdb=" C4 CWY B 902 " pdb=" C7 CWY B 902 " both_signs ideal model delta sigma weight residual True 2.64 1.82 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C3 CWY A 902 " pdb=" C1 CWY A 902 " pdb=" C4 CWY A 902 " pdb=" C6 CWY A 902 " both_signs ideal model delta sigma weight residual True 2.61 2.03 0.58 2.00e-01 2.50e+01 8.33e+00 ... (remaining 1709 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 247 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C VAL B 247 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL B 247 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY B 248 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 247 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C VAL A 247 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL A 247 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY A 248 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 637 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO B 638 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 638 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 638 " 0.035 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3455 2.83 - 3.35: 8512 3.35 - 3.87: 15505 3.87 - 4.38: 16996 4.38 - 4.90: 28562 Nonbonded interactions: 73030 Sorted by model distance: nonbonded pdb=" O SER A 250 " pdb=" OG SER A 250 " model vdw 2.318 2.440 nonbonded pdb=" O SER B 250 " pdb=" OG SER B 250 " model vdw 2.318 2.440 nonbonded pdb=" OG SER B 149 " pdb=" O2 CWY B 902 " model vdw 2.321 2.440 nonbonded pdb=" OG SER A 149 " pdb=" O2 CWY A 902 " model vdw 2.323 2.440 nonbonded pdb=" O SER B 100 " pdb=" OG SER B 100 " model vdw 2.327 2.440 ... (remaining 73025 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' selection = chain 'B' } 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 7.190 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 30.890 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.006 0.222 10180 Z= 0.379 Angle : 1.033 28.282 13968 Z= 0.544 Chirality : 0.064 0.823 1712 Planarity : 0.006 0.062 1826 Dihedral : 14.904 88.913 3284 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.81 % Favored : 88.92 % Rotamer: Outliers : 0.73 % Allowed : 7.56 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -6.08 (0.15), residues: 1462 helix: -4.83 (0.07), residues: 508 sheet: -4.23 (0.29), residues: 164 loop : -3.46 (0.18), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 486 HIS 0.006 0.001 HIS B 94 PHE 0.015 0.001 PHE B 45 TYR 0.012 0.001 TYR B 539 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 PHE cc_start: 0.8383 (m-10) cc_final: 0.7977 (m-80) REVERT: B 630 PHE cc_start: 0.8335 (m-10) cc_final: 0.7912 (m-80) outliers start: 6 outliers final: 0 residues processed: 143 average time/residue: 0.1906 time to fit residues: 40.1529 Evaluate side-chains 105 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 30.0000 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 70 optimal weight: 0.0670 chunk 86 optimal weight: 0.8980 chunk 134 optimal weight: 20.0000 overall best weight: 1.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 80 ASN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 GLN A 238 ASN A 467 ASN A 766 ASN B 48 ASN B 80 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN B 238 ASN B 467 ASN B 766 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10180 Z= 0.331 Angle : 0.692 9.989 13968 Z= 0.365 Chirality : 0.045 0.156 1712 Planarity : 0.005 0.064 1826 Dihedral : 9.941 81.554 1654 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.76 % Favored : 88.10 % Rotamer: Outliers : 3.66 % Allowed : 13.78 % Favored : 82.56 % 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: -5.60 (0.17), residues: 1462 helix: -4.16 (0.12), residues: 546 sheet: -3.86 (0.33), residues: 168 loop : -3.31 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 350 HIS 0.004 0.001 HIS A 485 PHE 0.019 0.002 PHE B 471 TYR 0.013 0.002 TYR B 466 ARG 0.009 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.8106 (t80) cc_final: 0.7766 (t80) REVERT: A 204 ILE cc_start: 0.8923 (tp) cc_final: 0.8607 (tp) REVERT: A 630 PHE cc_start: 0.8487 (m-10) cc_final: 0.8064 (m-80) REVERT: B 104 TYR cc_start: 0.8106 (t80) cc_final: 0.7773 (t80) REVERT: B 204 ILE cc_start: 0.8923 (tp) cc_final: 0.8608 (tp) REVERT: B 630 PHE cc_start: 0.8464 (m-10) cc_final: 0.8031 (m-80) outliers start: 30 outliers final: 20 residues processed: 125 average time/residue: 0.1743 time to fit residues: 33.6354 Evaluate side-chains 122 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 771 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.0270 chunk 134 optimal weight: 30.0000 chunk 145 optimal weight: 0.0040 chunk 119 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.4652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10180 Z= 0.157 Angle : 0.587 8.093 13968 Z= 0.310 Chirality : 0.042 0.151 1712 Planarity : 0.004 0.044 1826 Dihedral : 8.733 81.940 1654 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.12 % Favored : 89.74 % Rotamer: Outliers : 3.17 % Allowed : 16.46 % Favored : 80.37 % 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: -4.93 (0.18), residues: 1462 helix: -3.46 (0.16), residues: 536 sheet: -3.57 (0.34), residues: 180 loop : -3.02 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 554 HIS 0.004 0.001 HIS A 94 PHE 0.013 0.001 PHE A 598 TYR 0.022 0.001 TYR A 537 ARG 0.002 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.7899 (t80) cc_final: 0.7699 (t80) REVERT: A 204 ILE cc_start: 0.8847 (tp) cc_final: 0.8542 (tp) REVERT: A 630 PHE cc_start: 0.8497 (m-10) cc_final: 0.8088 (m-80) REVERT: B 204 ILE cc_start: 0.8844 (tp) cc_final: 0.8543 (tp) REVERT: B 630 PHE cc_start: 0.8478 (m-10) cc_final: 0.8063 (m-80) outliers start: 26 outliers final: 24 residues processed: 122 average time/residue: 0.1722 time to fit residues: 32.3054 Evaluate side-chains 128 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 660 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 0.2980 chunk 69 optimal weight: 0.0020 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10180 Z= 0.321 Angle : 0.652 9.003 13968 Z= 0.343 Chirality : 0.044 0.155 1712 Planarity : 0.004 0.040 1826 Dihedral : 9.044 82.769 1654 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.45 % Favored : 87.41 % Rotamer: Outliers : 4.39 % Allowed : 19.02 % Favored : 76.59 % 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: -4.61 (0.19), residues: 1462 helix: -3.04 (0.18), residues: 536 sheet: -3.40 (0.37), residues: 168 loop : -2.99 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 303 HIS 0.004 0.001 HIS B 485 PHE 0.022 0.002 PHE B 471 TYR 0.017 0.002 TYR A 539 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 104 TYR cc_start: 0.8288 (t80) cc_final: 0.7905 (t80) REVERT: A 204 ILE cc_start: 0.8901 (tp) cc_final: 0.8624 (tp) REVERT: A 400 MET cc_start: 0.7878 (tpp) cc_final: 0.7429 (tpt) REVERT: A 630 PHE cc_start: 0.8503 (m-10) cc_final: 0.8079 (m-80) REVERT: B 104 TYR cc_start: 0.8299 (t80) cc_final: 0.7913 (t80) REVERT: B 204 ILE cc_start: 0.8901 (tp) cc_final: 0.8621 (tp) REVERT: B 400 MET cc_start: 0.7880 (tpp) cc_final: 0.7413 (tpt) REVERT: B 630 PHE cc_start: 0.8473 (m-10) cc_final: 0.8045 (m-80) outliers start: 36 outliers final: 27 residues processed: 128 average time/residue: 0.1858 time to fit residues: 36.3032 Evaluate side-chains 131 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 771 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 0.0050 chunk 128 optimal weight: 30.0000 chunk 36 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10180 Z= 0.181 Angle : 0.585 7.635 13968 Z= 0.308 Chirality : 0.042 0.156 1712 Planarity : 0.003 0.039 1826 Dihedral : 8.371 85.386 1654 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.05 % Favored : 89.81 % Rotamer: Outliers : 3.78 % Allowed : 20.98 % Favored : 75.24 % 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: -4.25 (0.20), residues: 1462 helix: -2.69 (0.20), residues: 528 sheet: -3.26 (0.35), residues: 192 loop : -2.77 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 529 HIS 0.003 0.001 HIS B 94 PHE 0.009 0.001 PHE B 295 TYR 0.010 0.001 TYR B 539 ARG 0.002 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.8121 (t80) cc_final: 0.7785 (t80) REVERT: A 204 ILE cc_start: 0.8916 (tp) cc_final: 0.8667 (tp) REVERT: A 630 PHE cc_start: 0.8469 (m-10) cc_final: 0.8058 (m-80) REVERT: B 104 TYR cc_start: 0.8118 (t80) cc_final: 0.7779 (t80) REVERT: B 204 ILE cc_start: 0.8918 (tp) cc_final: 0.8662 (tp) REVERT: B 630 PHE cc_start: 0.8449 (m-10) cc_final: 0.8024 (m-80) outliers start: 31 outliers final: 24 residues processed: 124 average time/residue: 0.1665 time to fit residues: 31.8330 Evaluate side-chains 124 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 660 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 9.9990 chunk 128 optimal weight: 30.0000 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 0.0670 chunk 35 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10180 Z= 0.305 Angle : 0.634 8.254 13968 Z= 0.332 Chirality : 0.044 0.149 1712 Planarity : 0.004 0.038 1826 Dihedral : 8.738 87.649 1654 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.52 % Favored : 87.35 % Rotamer: Outliers : 4.63 % Allowed : 20.49 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.20), residues: 1462 helix: -2.48 (0.20), residues: 540 sheet: -3.18 (0.35), residues: 190 loop : -2.82 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 529 HIS 0.004 0.001 HIS B 485 PHE 0.016 0.002 PHE B 471 TYR 0.021 0.002 TYR B 537 ARG 0.003 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 96 time to evaluate : 1.166 Fit side-chains REVERT: A 104 TYR cc_start: 0.8272 (t80) cc_final: 0.7940 (t80) REVERT: A 204 ILE cc_start: 0.8990 (tp) cc_final: 0.8731 (tp) REVERT: A 400 MET cc_start: 0.7820 (tpp) cc_final: 0.7364 (tpt) REVERT: A 630 PHE cc_start: 0.8491 (m-10) cc_final: 0.8078 (m-80) REVERT: B 104 TYR cc_start: 0.8278 (t80) cc_final: 0.7985 (t80) REVERT: B 204 ILE cc_start: 0.8985 (tp) cc_final: 0.8734 (tp) REVERT: B 400 MET cc_start: 0.7816 (tpp) cc_final: 0.7334 (tpt) REVERT: B 630 PHE cc_start: 0.8492 (m-10) cc_final: 0.8068 (m-80) outliers start: 38 outliers final: 28 residues processed: 123 average time/residue: 0.1748 time to fit residues: 32.9758 Evaluate side-chains 123 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 771 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10180 Z= 0.177 Angle : 0.573 6.636 13968 Z= 0.301 Chirality : 0.042 0.157 1712 Planarity : 0.003 0.037 1826 Dihedral : 8.048 88.997 1654 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.71 % Favored : 90.15 % Rotamer: Outliers : 3.54 % Allowed : 21.95 % Favored : 74.51 % 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: -3.85 (0.21), residues: 1462 helix: -2.25 (0.21), residues: 542 sheet: -3.03 (0.35), residues: 192 loop : -2.63 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 529 HIS 0.003 0.001 HIS A 94 PHE 0.009 0.001 PHE B 295 TYR 0.008 0.001 TYR B 539 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.8160 (t80) cc_final: 0.7865 (t80) REVERT: A 204 ILE cc_start: 0.8952 (tp) cc_final: 0.8702 (tp) REVERT: A 630 PHE cc_start: 0.8493 (m-10) cc_final: 0.8050 (m-80) REVERT: B 104 TYR cc_start: 0.8161 (t80) cc_final: 0.7862 (t80) REVERT: B 204 ILE cc_start: 0.8957 (tp) cc_final: 0.8712 (tp) REVERT: B 630 PHE cc_start: 0.8489 (m-10) cc_final: 0.8046 (m-80) outliers start: 29 outliers final: 26 residues processed: 126 average time/residue: 0.1709 time to fit residues: 33.3896 Evaluate side-chains 125 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10180 Z= 0.180 Angle : 0.574 6.657 13968 Z= 0.300 Chirality : 0.042 0.144 1712 Planarity : 0.003 0.037 1826 Dihedral : 7.637 85.304 1654 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.94 % Favored : 88.92 % Rotamer: Outliers : 4.76 % Allowed : 21.71 % Favored : 73.54 % 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: -3.59 (0.21), residues: 1462 helix: -2.09 (0.22), residues: 546 sheet: -2.63 (0.39), residues: 174 loop : -2.53 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 529 HIS 0.003 0.001 HIS A 94 PHE 0.016 0.001 PHE B 598 TYR 0.006 0.001 TYR B 539 ARG 0.002 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 103 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.8153 (t80) cc_final: 0.7885 (t80) REVERT: A 204 ILE cc_start: 0.8952 (tp) cc_final: 0.8690 (tp) REVERT: A 303 TRP cc_start: 0.8917 (t60) cc_final: 0.8612 (t60) REVERT: A 630 PHE cc_start: 0.8493 (m-10) cc_final: 0.8041 (m-80) REVERT: B 104 TYR cc_start: 0.8153 (t80) cc_final: 0.7879 (t80) REVERT: B 204 ILE cc_start: 0.8949 (tp) cc_final: 0.8681 (tp) REVERT: B 303 TRP cc_start: 0.8915 (t60) cc_final: 0.8626 (t60) REVERT: B 630 PHE cc_start: 0.8495 (m-10) cc_final: 0.8044 (m-80) outliers start: 39 outliers final: 36 residues processed: 132 average time/residue: 0.1679 time to fit residues: 34.4487 Evaluate side-chains 140 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 485 HIS Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 771 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.0670 chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10180 Z= 0.234 Angle : 0.594 6.649 13968 Z= 0.312 Chirality : 0.043 0.141 1712 Planarity : 0.003 0.038 1826 Dihedral : 7.683 82.750 1654 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.22 % Favored : 88.65 % Rotamer: Outliers : 4.63 % Allowed : 21.95 % Favored : 73.41 % 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: -3.49 (0.21), residues: 1462 helix: -2.03 (0.22), residues: 546 sheet: -2.52 (0.39), residues: 170 loop : -2.48 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 486 HIS 0.003 0.001 HIS A 94 PHE 0.014 0.001 PHE A 598 TYR 0.009 0.001 TYR A 186 ARG 0.002 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 102 time to evaluate : 1.034 Fit side-chains REVERT: A 204 ILE cc_start: 0.8990 (tp) cc_final: 0.8707 (tp) REVERT: A 400 MET cc_start: 0.7757 (tpp) cc_final: 0.7331 (tpt) REVERT: A 630 PHE cc_start: 0.8512 (m-10) cc_final: 0.8056 (m-80) REVERT: B 204 ILE cc_start: 0.8981 (tp) cc_final: 0.8707 (tp) REVERT: B 400 MET cc_start: 0.7749 (tpp) cc_final: 0.7329 (tpt) REVERT: B 630 PHE cc_start: 0.8492 (m-10) cc_final: 0.8031 (m-80) outliers start: 38 outliers final: 34 residues processed: 128 average time/residue: 0.1643 time to fit residues: 32.6779 Evaluate side-chains 136 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 102 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 771 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 135 optimal weight: 0.0000 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 overall best weight: 0.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10180 Z= 0.161 Angle : 0.569 6.665 13968 Z= 0.298 Chirality : 0.042 0.143 1712 Planarity : 0.003 0.038 1826 Dihedral : 7.210 80.233 1654 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.85 % Favored : 90.01 % Rotamer: Outliers : 4.02 % Allowed : 22.80 % Favored : 73.17 % 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: -3.35 (0.22), residues: 1462 helix: -1.91 (0.22), residues: 544 sheet: -2.58 (0.39), residues: 174 loop : -2.35 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 486 HIS 0.003 0.001 HIS B 94 PHE 0.017 0.001 PHE B 598 TYR 0.009 0.001 TYR A 186 ARG 0.002 0.000 ARG B 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 108 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.8129 (t80) cc_final: 0.7887 (t80) REVERT: A 303 TRP cc_start: 0.8885 (t60) cc_final: 0.8588 (t60) REVERT: A 630 PHE cc_start: 0.8499 (m-10) cc_final: 0.8030 (m-80) REVERT: B 104 TYR cc_start: 0.8154 (t80) cc_final: 0.7876 (t80) REVERT: B 303 TRP cc_start: 0.8881 (t60) cc_final: 0.8596 (t60) REVERT: B 630 PHE cc_start: 0.8486 (m-10) cc_final: 0.8011 (m-80) outliers start: 33 outliers final: 33 residues processed: 131 average time/residue: 0.1681 time to fit residues: 34.1124 Evaluate side-chains 139 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 771 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 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 = 0.4706 r_free = 0.4706 target = 0.218223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.174840 restraints weight = 14119.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.168412 restraints weight = 21766.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.170977 restraints weight = 16411.946| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10180 Z= 0.199 Angle : 0.579 6.642 13968 Z= 0.303 Chirality : 0.042 0.128 1712 Planarity : 0.003 0.038 1826 Dihedral : 7.259 79.099 1654 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.81 % Favored : 89.06 % Rotamer: Outliers : 4.51 % Allowed : 22.44 % Favored : 73.05 % 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: -3.33 (0.22), residues: 1462 helix: -1.84 (0.22), residues: 548 sheet: -2.59 (0.38), residues: 176 loop : -2.37 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 486 HIS 0.003 0.001 HIS B 94 PHE 0.016 0.001 PHE A 598 TYR 0.008 0.001 TYR A 186 ARG 0.003 0.000 ARG B 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1925.92 seconds wall clock time: 35 minutes 25.10 seconds (2125.10 seconds total)