Starting phenix.real_space_refine on Mon Dec 30 06:12:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0h_37979/12_2024/8x0h_37979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0h_37979/12_2024/8x0h_37979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x0h_37979/12_2024/8x0h_37979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0h_37979/12_2024/8x0h_37979.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0h_37979/12_2024/8x0h_37979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0h_37979/12_2024/8x0h_37979.cif" } resolution = 4.1 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= 0.011 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 118 5.16 5 C 7914 2.51 5 N 2049 2.21 5 O 2236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12317 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6140 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 33, 'TRANS': 746} Chain breaks: 1 Chain: "B" Number of atoms: 6123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6123 Classifications: {'peptide': 778} Link IDs: {'PTRANS': 33, 'TRANS': 744} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'QUS': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'QUS': 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: 8.65, per 1000 atoms: 0.70 Number of scatterers: 12317 At special positions: 0 Unit cell: (73.92, 111.72, 186.48, 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 118 16.00 O 2236 8.00 N 2049 7.00 C 7914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " 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 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 210 " " NAG B 901 " - " ASN B 210 " Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.7 seconds 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2908 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 49.8% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.587A pdb=" N ALA A 105 " --> pdb=" O HIS A 101 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.732A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.553A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 198 through 209 Processing helix chain 'A' and resid 221 through 239 removed outlier: 4.132A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.602A pdb=" N PHE A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.826A pdb=" N VAL A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.645A pdb=" N VAL A 313 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 397 through 419 removed outlier: 3.697A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 416 " --> pdb=" O HIS A 412 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 418 " --> pdb=" O MET A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.600A pdb=" N LEU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 563 Processing helix chain 'A' and resid 577 through 603 removed outlier: 3.649A pdb=" N ILE A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.713A pdb=" N SER A 612 " --> pdb=" O PRO A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 636 removed outlier: 4.286A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 679 removed outlier: 4.000A pdb=" N TYR A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 4.030A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 679 " --> pdb=" O GLY A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 715 removed outlier: 3.639A pdb=" N VAL A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 742 removed outlier: 3.669A pdb=" N VAL A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 741 " --> pdb=" O ASN A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 762 removed outlier: 3.759A pdb=" N ASN A 747 " --> pdb=" O PRO A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 793 removed outlier: 4.670A pdb=" N PHE A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) removed outlier: 4.175A 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 818 removed outlier: 3.795A pdb=" N MET A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N CYS A 803 " --> pdb=" O ALA A 799 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 804 " --> pdb=" O ILE A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 827 removed outlier: 3.610A pdb=" N VAL A 822 " --> pdb=" O PHE A 818 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 823 " --> pdb=" O VAL A 819 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 826 " --> pdb=" O VAL A 822 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 827 " --> pdb=" O TYR A 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 removed outlier: 4.090A pdb=" N VAL B 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 81 Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 151 through 166 removed outlier: 4.215A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 194 through 209 removed outlier: 4.065A pdb=" N GLN B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.941A pdb=" N GLU B 225 " --> pdb=" O GLY B 221 " (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 279 through 294 Processing helix chain 'B' and resid 334 through 344 removed outlier: 3.867A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 363 removed outlier: 3.979A pdb=" N GLN B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP B 359 " --> pdb=" O PHE B 355 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLN B 360 " --> pdb=" O GLN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 419 removed outlier: 3.574A pdb=" N ILE B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 433 through 443 removed outlier: 4.031A pdb=" N LEU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 563 Processing helix chain 'B' and resid 578 through 581 removed outlier: 3.558A pdb=" N ILE B 581 " --> pdb=" O PRO B 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 578 through 581' Processing helix chain 'B' and resid 582 through 604 Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.780A pdb=" N SER B 612 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 613 " --> pdb=" O VAL B 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 609 through 613' Processing helix chain 'B' and resid 615 through 635 Processing helix chain 'B' and resid 640 through 679 removed outlier: 3.944A pdb=" N TYR B 645 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 648 " --> pdb=" O CYS B 644 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 4.577A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY B 675 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS B 678 " --> pdb=" O ALA B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 715 removed outlier: 3.683A pdb=" N VAL B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 705 " --> pdb=" O ILE B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 762 removed outlier: 3.891A pdb=" N ALA B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Proline residue: B 743 - end of helix removed outlier: 3.847A pdb=" N ALA B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N CYS B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 769 Processing helix chain 'B' and resid 770 through 787 removed outlier: 3.826A pdb=" N ILE B 774 " --> pdb=" O GLU B 770 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE B 776 " --> pdb=" O LYS B 772 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR B 780 " --> pdb=" O PHE B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 793 removed outlier: 4.464A pdb=" N ILE B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 818 removed outlier: 3.983A pdb=" N LEU B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 5.875A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 214 removed outlier: 3.899A pdb=" N VAL A 214 " --> pdb=" O CYS A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 219 removed outlier: 6.456A pdb=" N HIS A 218 " --> pdb=" O ILE A 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA6, first strand: chain 'A' and resid 485 through 486 Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 556 through 558 Processing sheet with id=AB1, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 39 removed outlier: 5.800A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 147 removed outlier: 6.959A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 213 through 214 Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 275 removed outlier: 3.679A pdb=" N VAL B 274 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 302 " --> pdb=" O VAL B 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 326 through 329 removed outlier: 3.866A pdb=" N MET B 469 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 470 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AB8, first strand: chain 'B' and resid 485 through 488 Processing sheet with id=AB9, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AC1, first strand: chain 'B' and resid 541 through 545 removed outlier: 6.241A pdb=" N THR B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.525A pdb=" N TYR B 730 " --> pdb=" O ASP B 722 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1482 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: 4.03 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2226 1.33 - 1.45: 3183 1.45 - 1.57: 7020 1.57 - 1.69: 0 1.69 - 1.82: 170 Bond restraints: 12599 Sorted by residual: bond pdb=" C04 QUS A 902 " pdb=" N14 QUS A 902 " ideal model delta sigma weight residual 1.380 1.341 0.039 2.00e-02 2.50e+03 3.79e+00 bond pdb=" C04 QUS B 902 " pdb=" N14 QUS B 902 " ideal model delta sigma weight residual 1.380 1.344 0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" CG1 ILE A 703 " pdb=" CD1 ILE A 703 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.47e+00 bond pdb=" CB MET A 202 " pdb=" CG MET A 202 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" C02 QUS B 902 " pdb=" NP3 QUS B 902 " ideal model delta sigma weight residual 1.460 1.488 -0.028 2.00e-02 2.50e+03 1.96e+00 ... (remaining 12594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 16663 1.94 - 3.89: 346 3.89 - 5.83: 35 5.83 - 7.77: 14 7.77 - 9.72: 7 Bond angle restraints: 17065 Sorted by residual: angle pdb=" N VAL B 104 " pdb=" CA VAL B 104 " pdb=" C VAL B 104 " ideal model delta sigma weight residual 112.29 106.95 5.34 9.40e-01 1.13e+00 3.23e+01 angle pdb=" N VAL B 144 " pdb=" CA VAL B 144 " pdb=" C VAL B 144 " ideal model delta sigma weight residual 113.53 108.02 5.51 9.80e-01 1.04e+00 3.16e+01 angle pdb=" C VAL B 570 " pdb=" N GLN B 571 " pdb=" CA GLN B 571 " ideal model delta sigma weight residual 121.54 129.49 -7.95 1.91e+00 2.74e-01 1.73e+01 angle pdb=" C TYR B 209 " pdb=" N ASN B 210 " pdb=" CA ASN B 210 " ideal model delta sigma weight residual 122.46 127.12 -4.66 1.41e+00 5.03e-01 1.09e+01 angle pdb=" C03 QUS B 902 " pdb=" N14 QUS B 902 " pdb=" O20 QUS B 902 " ideal model delta sigma weight residual 112.77 122.49 -9.72 3.00e+00 1.11e-01 1.05e+01 ... (remaining 17060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.57: 6919 20.57 - 41.15: 604 41.15 - 61.72: 70 61.72 - 82.29: 21 82.29 - 102.87: 8 Dihedral angle restraints: 7622 sinusoidal: 3086 harmonic: 4536 Sorted by residual: dihedral pdb=" CB CYS B 644 " pdb=" SG CYS B 644 " pdb=" SG CYS B 733 " pdb=" CB CYS B 733 " ideal model delta sinusoidal sigma weight residual -86.00 -176.16 90.16 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS A 537 " pdb=" SG CYS A 537 " pdb=" SG CYS A 549 " pdb=" CB CYS A 549 " ideal model delta sinusoidal sigma weight residual -86.00 -164.71 78.71 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" CB CYS A 644 " pdb=" SG CYS A 644 " pdb=" SG CYS A 733 " pdb=" CB CYS A 733 " ideal model delta sinusoidal sigma weight residual -86.00 -158.78 72.78 1 1.00e+01 1.00e-02 6.76e+01 ... (remaining 7619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1346 0.043 - 0.086: 422 0.086 - 0.128: 135 0.128 - 0.171: 9 0.171 - 0.214: 3 Chirality restraints: 1915 Sorted by residual: chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 210 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 210 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CA GLU A 579 " pdb=" N GLU A 579 " pdb=" C GLU A 579 " pdb=" CB GLU A 579 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.08e-01 ... (remaining 1912 not shown) Planarity restraints: 2149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 268 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.79e+00 pdb=" N PRO B 269 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 269 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 269 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 500 " 0.016 2.00e-02 2.50e+03 1.24e-02 3.86e+00 pdb=" CG TRP B 500 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 500 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 500 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 500 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 500 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 500 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 500 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 500 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 500 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 568 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B 569 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 569 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 569 " 0.027 5.00e-02 4.00e+02 ... (remaining 2146 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 167 2.62 - 3.19: 12055 3.19 - 3.76: 19739 3.76 - 4.33: 26160 4.33 - 4.90: 41555 Nonbonded interactions: 99676 Sorted by model distance: nonbonded pdb=" O CYS B 276 " pdb=" OG SER B 304 " model vdw 2.051 3.040 nonbonded pdb=" NH1 ARG B 272 " pdb=" O GLU B 298 " model vdw 2.207 3.120 nonbonded pdb=" O4 NAG A 901 " pdb=" O7 NAG A 901 " model vdw 2.207 3.040 nonbonded pdb=" O PHE B 231 " pdb=" OG SER B 235 " model vdw 2.219 3.040 nonbonded pdb=" O GLY B 324 " pdb=" OG1 THR B 326 " model vdw 2.232 3.040 ... (remaining 99671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 116 or resid 142 through 827 or resid 901 throu \ gh 902)) 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: 3.640 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.830 Find NCS groups from input model: 0.480 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12599 Z= 0.273 Angle : 0.688 9.715 17065 Z= 0.358 Chirality : 0.045 0.214 1915 Planarity : 0.004 0.065 2147 Dihedral : 14.994 102.866 4654 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.84 % Favored : 89.10 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.21), residues: 1550 helix: 0.31 (0.20), residues: 621 sheet: -3.34 (0.46), residues: 91 loop : -2.09 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 500 HIS 0.004 0.001 HIS A 267 PHE 0.026 0.002 PHE B 299 TYR 0.021 0.001 TYR A 779 ARG 0.011 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: B 407 MET cc_start: 0.6252 (tpt) cc_final: 0.5829 (mmm) REVERT: B 429 MET cc_start: 0.7767 (mpp) cc_final: 0.7256 (tpt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2123 time to fit residues: 43.5232 Evaluate side-chains 107 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.4980 chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN ** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12599 Z= 0.357 Angle : 0.696 7.105 17065 Z= 0.366 Chirality : 0.046 0.196 1915 Planarity : 0.005 0.047 2147 Dihedral : 7.271 73.548 1754 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.90 % Favored : 88.97 % Rotamer: Outliers : 0.07 % Allowed : 8.40 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.21), residues: 1550 helix: 0.19 (0.20), residues: 637 sheet: -2.60 (0.44), residues: 116 loop : -2.17 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 500 HIS 0.009 0.002 HIS B 412 PHE 0.032 0.002 PHE B 299 TYR 0.016 0.002 TYR A 779 ARG 0.005 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.2440 (mmt) cc_final: 0.2211 (mmt) REVERT: B 407 MET cc_start: 0.6212 (tpt) cc_final: 0.5943 (mmm) REVERT: B 429 MET cc_start: 0.7895 (mpp) cc_final: 0.7165 (tpt) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.2331 time to fit residues: 47.9424 Evaluate side-chains 105 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 413 ASN ** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12599 Z= 0.407 Angle : 0.737 8.520 17065 Z= 0.387 Chirality : 0.047 0.239 1915 Planarity : 0.005 0.047 2147 Dihedral : 6.595 71.343 1754 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.87 % Favored : 88.00 % Rotamer: Outliers : 0.07 % Allowed : 6.98 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.21), residues: 1550 helix: -0.09 (0.19), residues: 638 sheet: -2.69 (0.44), residues: 110 loop : -2.24 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 307 HIS 0.006 0.002 HIS B 44 PHE 0.030 0.003 PHE A 277 TYR 0.018 0.002 TYR A 645 ARG 0.004 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8550 (tpp) cc_final: 0.8315 (tpp) REVERT: A 96 ARG cc_start: 0.7928 (mtt-85) cc_final: 0.7658 (mtt-85) REVERT: A 776 PHE cc_start: 0.7911 (m-80) cc_final: 0.7702 (m-80) REVERT: B 429 MET cc_start: 0.7992 (mpp) cc_final: 0.7086 (tpt) REVERT: B 442 MET cc_start: 0.7330 (tpt) cc_final: 0.7062 (ptp) REVERT: B 812 VAL cc_start: 0.9159 (p) cc_final: 0.8780 (p) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.2217 time to fit residues: 43.8639 Evaluate side-chains 106 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 7.9990 chunk 106 optimal weight: 0.0170 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 0.0060 chunk 149 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN B 159 GLN B 160 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12599 Z= 0.177 Angle : 0.614 7.951 17065 Z= 0.313 Chirality : 0.044 0.212 1915 Planarity : 0.004 0.043 2147 Dihedral : 5.834 72.542 1754 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.52 % Favored : 91.35 % Rotamer: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.21), residues: 1550 helix: 0.51 (0.20), residues: 639 sheet: -2.66 (0.44), residues: 113 loop : -2.15 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 532 HIS 0.004 0.001 HIS B 45 PHE 0.019 0.002 PHE A 337 TYR 0.015 0.001 TYR A 779 ARG 0.006 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 778 MET cc_start: 0.8126 (mmp) cc_final: 0.7714 (mmp) REVERT: B 228 MET cc_start: 0.6143 (mmt) cc_final: 0.5892 (mmt) REVERT: B 407 MET cc_start: 0.6165 (tpt) cc_final: 0.5819 (mmm) REVERT: B 442 MET cc_start: 0.7282 (tpt) cc_final: 0.6878 (ptp) REVERT: B 720 MET cc_start: 0.8597 (ppp) cc_final: 0.7353 (ppp) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.2332 time to fit residues: 53.5776 Evaluate side-chains 105 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN ** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12599 Z= 0.377 Angle : 0.712 8.906 17065 Z= 0.373 Chirality : 0.047 0.239 1915 Planarity : 0.005 0.048 2147 Dihedral : 6.289 72.160 1754 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.90 % Favored : 88.97 % Rotamer: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.21), residues: 1550 helix: 0.17 (0.20), residues: 641 sheet: -2.96 (0.44), residues: 110 loop : -2.21 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 307 HIS 0.006 0.001 HIS B 44 PHE 0.035 0.002 PHE B 299 TYR 0.016 0.002 TYR A 405 ARG 0.007 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8620 (tpp) cc_final: 0.8403 (tpp) REVERT: A 429 MET cc_start: 0.8660 (mpp) cc_final: 0.8358 (mpp) REVERT: B 429 MET cc_start: 0.7917 (mpp) cc_final: 0.7099 (tpt) REVERT: B 442 MET cc_start: 0.7258 (tpt) cc_final: 0.6887 (ptp) REVERT: B 664 THR cc_start: 0.8733 (t) cc_final: 0.8427 (p) outliers start: 2 outliers final: 0 residues processed: 134 average time/residue: 0.2114 time to fit residues: 44.0067 Evaluate side-chains 101 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 413 ASN ** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12599 Z= 0.317 Angle : 0.681 10.011 17065 Z= 0.355 Chirality : 0.046 0.222 1915 Planarity : 0.004 0.047 2147 Dihedral : 6.155 72.724 1754 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.65 % Favored : 89.23 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.21), residues: 1550 helix: 0.18 (0.20), residues: 641 sheet: -3.15 (0.43), residues: 113 loop : -2.25 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 359 HIS 0.019 0.002 HIS B 412 PHE 0.026 0.002 PHE B 299 TYR 0.014 0.002 TYR A 645 ARG 0.008 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.8730 (mpp) cc_final: 0.8357 (mpp) REVERT: B 407 MET cc_start: 0.6216 (tpt) cc_final: 0.5868 (mmm) REVERT: B 429 MET cc_start: 0.7924 (mpp) cc_final: 0.7120 (tpt) REVERT: B 664 THR cc_start: 0.8704 (t) cc_final: 0.8391 (p) REVERT: B 720 MET cc_start: 0.8568 (ppp) cc_final: 0.7332 (ppp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2218 time to fit residues: 45.2517 Evaluate side-chains 104 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN B 45 HIS B 255 GLN B 267 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12599 Z= 0.249 Angle : 0.648 9.374 17065 Z= 0.335 Chirality : 0.045 0.207 1915 Planarity : 0.004 0.052 2147 Dihedral : 5.970 72.707 1754 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.19 % Favored : 89.68 % Rotamer: Outliers : 0.07 % Allowed : 2.08 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.21), residues: 1550 helix: 0.34 (0.20), residues: 641 sheet: -3.02 (0.45), residues: 113 loop : -2.24 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 359 HIS 0.007 0.001 HIS B 412 PHE 0.023 0.002 PHE B 633 TYR 0.012 0.001 TYR A 645 ARG 0.010 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 429 MET cc_start: 0.8755 (mpp) cc_final: 0.8528 (mpp) REVERT: A 778 MET cc_start: 0.8067 (mmp) cc_final: 0.7591 (mmp) REVERT: B 407 MET cc_start: 0.6118 (tpt) cc_final: 0.5839 (mmm) REVERT: B 429 MET cc_start: 0.7959 (mpp) cc_final: 0.7115 (tpt) REVERT: B 664 THR cc_start: 0.8667 (t) cc_final: 0.8363 (p) REVERT: B 720 MET cc_start: 0.8590 (ppp) cc_final: 0.7385 (ppp) REVERT: B 803 CYS cc_start: 0.8653 (m) cc_final: 0.8452 (m) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.2093 time to fit residues: 45.0180 Evaluate side-chains 108 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 413 ASN B 255 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12599 Z= 0.220 Angle : 0.631 8.970 17065 Z= 0.325 Chirality : 0.044 0.199 1915 Planarity : 0.004 0.045 2147 Dihedral : 5.826 72.725 1754 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.48 % Favored : 90.39 % Rotamer: Outliers : 0.07 % Allowed : 1.19 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.21), residues: 1550 helix: 0.48 (0.20), residues: 640 sheet: -2.91 (0.45), residues: 113 loop : -2.22 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 359 HIS 0.003 0.001 HIS A 412 PHE 0.018 0.002 PHE B 299 TYR 0.013 0.001 TYR B 187 ARG 0.007 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8588 (tpp) cc_final: 0.8336 (tpp) REVERT: A 429 MET cc_start: 0.8729 (mpp) cc_final: 0.8457 (mpp) REVERT: A 619 TYR cc_start: 0.6603 (t80) cc_final: 0.6385 (t80) REVERT: A 778 MET cc_start: 0.8124 (mmp) cc_final: 0.7669 (mmp) REVERT: B 407 MET cc_start: 0.6032 (tpt) cc_final: 0.5793 (mmm) REVERT: B 429 MET cc_start: 0.7916 (mpp) cc_final: 0.7066 (tpt) REVERT: B 442 MET cc_start: 0.7649 (ptp) cc_final: 0.6770 (tpt) REVERT: B 664 THR cc_start: 0.8649 (t) cc_final: 0.8347 (p) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.2233 time to fit residues: 47.2128 Evaluate side-chains 109 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 413 ASN B 255 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 12599 Z= 0.308 Angle : 0.687 8.826 17065 Z= 0.356 Chirality : 0.046 0.204 1915 Planarity : 0.004 0.048 2147 Dihedral : 6.022 73.019 1754 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.16 % Favored : 88.71 % Rotamer: Outliers : 0.07 % Allowed : 1.11 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.21), residues: 1550 helix: 0.30 (0.20), residues: 641 sheet: -2.89 (0.47), residues: 104 loop : -2.23 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 359 HIS 0.005 0.001 HIS B 218 PHE 0.031 0.002 PHE A 112 TYR 0.028 0.002 TYR A 187 ARG 0.008 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8612 (tpp) cc_final: 0.8396 (tpp) REVERT: A 429 MET cc_start: 0.8733 (mpp) cc_final: 0.8455 (mpp) REVERT: B 407 MET cc_start: 0.6052 (tpt) cc_final: 0.5819 (mmm) REVERT: B 429 MET cc_start: 0.7900 (mpp) cc_final: 0.7033 (tpt) REVERT: B 442 MET cc_start: 0.7735 (ptp) cc_final: 0.6804 (tpp) REVERT: B 664 THR cc_start: 0.8693 (t) cc_final: 0.8383 (p) REVERT: B 720 MET cc_start: 0.8577 (ppp) cc_final: 0.7472 (ppp) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.2383 time to fit residues: 48.5916 Evaluate side-chains 108 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12599 Z= 0.297 Angle : 0.690 9.346 17065 Z= 0.356 Chirality : 0.046 0.215 1915 Planarity : 0.004 0.046 2147 Dihedral : 6.018 72.721 1754 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.23 % Favored : 88.65 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.21), residues: 1550 helix: 0.33 (0.20), residues: 638 sheet: -3.02 (0.46), residues: 106 loop : -2.20 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 359 HIS 0.005 0.001 HIS A 53 PHE 0.027 0.002 PHE A 112 TYR 0.027 0.002 TYR A 187 ARG 0.006 0.000 ARG B 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8625 (tpp) cc_final: 0.8386 (tpp) REVERT: A 429 MET cc_start: 0.8735 (mpp) cc_final: 0.8439 (mpp) REVERT: A 477 ASP cc_start: 0.7927 (m-30) cc_final: 0.7539 (m-30) REVERT: A 720 MET cc_start: 0.8688 (ptm) cc_final: 0.8447 (ptm) REVERT: A 778 MET cc_start: 0.7991 (mmp) cc_final: 0.7409 (mmp) REVERT: B 407 MET cc_start: 0.6027 (tpt) cc_final: 0.5813 (mmm) REVERT: B 429 MET cc_start: 0.7934 (mpp) cc_final: 0.6997 (tpt) REVERT: B 442 MET cc_start: 0.7627 (ptp) cc_final: 0.6720 (tpp) REVERT: B 664 THR cc_start: 0.8686 (t) cc_final: 0.8386 (p) REVERT: B 720 MET cc_start: 0.8532 (ppp) cc_final: 0.7351 (ppp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2236 time to fit residues: 46.9264 Evaluate side-chains 109 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 393 GLN A 413 ASN B 108 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.118762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.098331 restraints weight = 37281.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.097577 restraints weight = 36126.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.098219 restraints weight = 34517.325| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12599 Z= 0.186 Angle : 0.647 9.484 17065 Z= 0.329 Chirality : 0.044 0.205 1915 Planarity : 0.004 0.044 2147 Dihedral : 5.752 71.280 1754 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.03 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1550 helix: 0.56 (0.20), residues: 641 sheet: -2.81 (0.44), residues: 122 loop : -2.14 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 359 HIS 0.006 0.001 HIS B 45 PHE 0.034 0.002 PHE A 112 TYR 0.023 0.001 TYR A 187 ARG 0.006 0.000 ARG B 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2237.06 seconds wall clock time: 42 minutes 30.94 seconds (2550.94 seconds total)