Starting phenix.real_space_refine on Sat Jan 18 14:37:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0h_37979/01_2025/8x0h_37979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0h_37979/01_2025/8x0h_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_37979/01_2025/8x0h_37979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0h_37979/01_2025/8x0h_37979.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0h_37979/01_2025/8x0h_37979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0h_37979/01_2025/8x0h_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 8.24, per 1000 atoms: 0.67 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: 2.99 Conformation dependent library (CDL) restraints added in 1.5 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: 1.29 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: 3.79 Time building geometry restraints manager: 3.44 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: 5.790 Set stop_for_unknowns flag: 0.010 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.480 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.170 ------------------------------------------------------------------------------- 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 : 1.330 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: 0.2114 time to fit residues: 43.5388 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 : 1.459 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.114469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.093894 restraints weight = 38220.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.093301 restraints weight = 43187.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.094061 restraints weight = 39149.875| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.2345 (mmt) cc_final: 0.2121 (mmt) REVERT: B 407 MET cc_start: 0.6195 (tpt) cc_final: 0.5928 (mmm) REVERT: B 429 MET cc_start: 0.7993 (mpp) cc_final: 0.7231 (tpt) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.2182 time to fit residues: 44.6637 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 : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 126 optimal weight: 8.9990 chunk 50 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.118450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.096906 restraints weight = 37596.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.097099 restraints weight = 31499.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.097816 restraints weight = 28854.544| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12599 Z= 0.179 Angle : 0.606 9.173 17065 Z= 0.311 Chirality : 0.043 0.219 1915 Planarity : 0.004 0.045 2147 Dihedral : 5.895 71.274 1754 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.52 % Favored : 91.35 % Rotamer: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.66 % 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: -1.45 (0.21), residues: 1550 helix: 0.59 (0.20), residues: 638 sheet: -2.60 (0.45), residues: 111 loop : -2.09 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 500 HIS 0.003 0.001 HIS A 412 PHE 0.015 0.001 PHE A 337 TYR 0.015 0.001 TYR A 779 ARG 0.006 0.000 ARG B 671 *********************** 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 151 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 688 MET cc_start: 0.6397 (mmt) cc_final: 0.6150 (mmt) REVERT: B 429 MET cc_start: 0.8021 (mpp) cc_final: 0.7124 (tpt) REVERT: B 442 MET cc_start: 0.7302 (tpt) cc_final: 0.7064 (ptp) REVERT: B 673 LEU cc_start: 0.7871 (mt) cc_final: 0.7427 (tt) REVERT: B 720 MET cc_start: 0.8626 (ppp) cc_final: 0.7440 (ppp) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.2145 time to fit residues: 49.2110 Evaluate side-chains 113 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.116410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.095474 restraints weight = 37842.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.094979 restraints weight = 38739.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.095781 restraints weight = 36677.635| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12599 Z= 0.266 Angle : 0.622 7.655 17065 Z= 0.324 Chirality : 0.044 0.207 1915 Planarity : 0.004 0.046 2147 Dihedral : 5.924 71.000 1754 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.87 % Favored : 90.00 % Rotamer: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.54 % 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: -1.51 (0.21), residues: 1550 helix: 0.54 (0.20), residues: 640 sheet: -2.75 (0.44), residues: 113 loop : -2.10 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 532 HIS 0.004 0.001 HIS B 44 PHE 0.025 0.002 PHE B 471 TYR 0.012 0.001 TYR A 779 ARG 0.007 0.000 ARG A 96 *********************** 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 135 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 688 MET cc_start: 0.6416 (mmt) cc_final: 0.6166 (mmt) REVERT: B 407 MET cc_start: 0.6203 (tpt) cc_final: 0.5883 (mmm) REVERT: B 442 MET cc_start: 0.7383 (tpt) cc_final: 0.6936 (ptp) REVERT: B 664 THR cc_start: 0.8649 (t) cc_final: 0.8356 (p) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.2121 time to fit residues: 44.3948 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 : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 112 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.117493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.097095 restraints weight = 37805.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.096631 restraints weight = 39409.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.097475 restraints weight = 35508.627| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12599 Z= 0.183 Angle : 0.591 7.208 17065 Z= 0.303 Chirality : 0.043 0.204 1915 Planarity : 0.004 0.047 2147 Dihedral : 5.695 70.825 1754 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.71 % Favored : 91.16 % Rotamer: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.73 % 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: -1.39 (0.21), residues: 1550 helix: 0.72 (0.20), residues: 639 sheet: -2.55 (0.44), residues: 122 loop : -2.12 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 532 HIS 0.004 0.001 HIS A 412 PHE 0.015 0.002 PHE A 337 TYR 0.012 0.001 TYR A 779 ARG 0.005 0.000 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 147 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: A 429 MET cc_start: 0.8536 (mpp) cc_final: 0.8273 (mpp) REVERT: A 688 MET cc_start: 0.6382 (mmt) cc_final: 0.6150 (mmt) REVERT: B 429 MET cc_start: 0.8018 (mpp) cc_final: 0.7041 (tpt) REVERT: B 442 MET cc_start: 0.7328 (tpt) cc_final: 0.6884 (ptp) REVERT: B 720 MET cc_start: 0.8579 (ppp) cc_final: 0.7424 (ppp) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2013 time to fit residues: 46.1717 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 : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 92 optimal weight: 0.0370 chunk 46 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 721 HIS B 45 HIS B 160 ASN ** 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 = 0.4018 r_free = 0.4018 target = 0.117381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.096392 restraints weight = 38046.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.095780 restraints weight = 37967.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.096718 restraints weight = 33601.394| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12599 Z= 0.218 Angle : 0.617 9.999 17065 Z= 0.317 Chirality : 0.044 0.213 1915 Planarity : 0.004 0.048 2147 Dihedral : 5.753 70.697 1754 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.29 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: -1.39 (0.21), residues: 1550 helix: 0.68 (0.20), residues: 642 sheet: -2.57 (0.43), residues: 122 loop : -2.09 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 307 HIS 0.003 0.001 HIS A 412 PHE 0.033 0.002 PHE A 112 TYR 0.013 0.001 TYR A 645 ARG 0.006 0.000 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 146 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 429 MET cc_start: 0.8604 (mpp) cc_final: 0.8293 (mpp) REVERT: A 688 MET cc_start: 0.6365 (mmt) cc_final: 0.6150 (mmt) REVERT: B 407 MET cc_start: 0.5970 (tpt) cc_final: 0.5671 (mmm) REVERT: B 429 MET cc_start: 0.8015 (mpp) cc_final: 0.7079 (tpt) REVERT: B 720 MET cc_start: 0.8601 (ppp) cc_final: 0.7379 (ppp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2041 time to fit residues: 46.3777 Evaluate side-chains 112 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 90 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 102 optimal weight: 0.0970 chunk 119 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN B 63 GLN B 255 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.115120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.094570 restraints weight = 37709.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.094264 restraints weight = 44022.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.095139 restraints weight = 38769.712| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 : 0.005 0.070 12599 Z= 0.342 Angle : 0.690 9.101 17065 Z= 0.359 Chirality : 0.046 0.202 1915 Planarity : 0.005 0.054 2147 Dihedral : 6.061 71.204 1754 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.35 % Favored : 88.52 % Rotamer: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.33 % 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: -1.71 (0.21), residues: 1550 helix: 0.36 (0.20), residues: 642 sheet: -2.71 (0.43), residues: 121 loop : -2.22 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 532 HIS 0.005 0.001 HIS B 44 PHE 0.029 0.002 PHE B 471 TYR 0.013 0.002 TYR A 645 ARG 0.008 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 139 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8653 (tpp) cc_final: 0.8411 (tpp) REVERT: A 234 MET cc_start: 0.8834 (ttm) cc_final: 0.8548 (mtp) REVERT: B 407 MET cc_start: 0.6041 (tpt) cc_final: 0.5762 (mmm) REVERT: B 429 MET cc_start: 0.7969 (mpp) cc_final: 0.7028 (tpt) REVERT: B 664 THR cc_start: 0.8662 (t) cc_final: 0.8374 (p) REVERT: B 720 MET cc_start: 0.8488 (ppp) cc_final: 0.7941 (ppp) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.2170 time to fit residues: 45.6900 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 : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 255 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 = 0.4022 r_free = 0.4022 target = 0.117410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.097080 restraints weight = 38480.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.096356 restraints weight = 43538.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.097263 restraints weight = 39156.939| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12599 Z= 0.215 Angle : 0.631 8.860 17065 Z= 0.324 Chirality : 0.044 0.203 1915 Planarity : 0.004 0.057 2147 Dihedral : 5.782 71.176 1754 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.97 % Favored : 90.90 % Rotamer: Outliers : 0.07 % Allowed : 1.26 % Favored : 98.66 % 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: -1.53 (0.21), residues: 1550 helix: 0.56 (0.20), residues: 642 sheet: -2.79 (0.44), residues: 121 loop : -2.14 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 532 HIS 0.003 0.001 HIS B 44 PHE 0.033 0.002 PHE A 112 TYR 0.012 0.001 TYR A 645 ARG 0.011 0.001 ARG A 291 *********************** 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 145 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8611 (tpp) cc_final: 0.8368 (tpp) REVERT: B 407 MET cc_start: 0.6053 (tpt) cc_final: 0.5818 (mmm) REVERT: B 429 MET cc_start: 0.8063 (mpp) cc_final: 0.7205 (tpt) REVERT: B 664 THR cc_start: 0.8682 (t) cc_final: 0.8358 (p) REVERT: B 720 MET cc_start: 0.8677 (ppp) cc_final: 0.8115 (ppp) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.2170 time to fit residues: 47.6535 Evaluate side-chains 111 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 145 optimal weight: 0.0050 chunk 45 optimal weight: 6.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.116591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.096628 restraints weight = 38180.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.095843 restraints weight = 49380.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.096785 restraints weight = 45460.255| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12599 Z= 0.271 Angle : 0.659 8.498 17065 Z= 0.340 Chirality : 0.045 0.197 1915 Planarity : 0.004 0.048 2147 Dihedral : 5.889 71.327 1754 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.32 % Favored : 89.55 % 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: -1.59 (0.21), residues: 1550 helix: 0.47 (0.20), residues: 642 sheet: -2.68 (0.47), residues: 112 loop : -2.17 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 532 HIS 0.005 0.001 HIS B 267 PHE 0.027 0.002 PHE A 112 TYR 0.013 0.001 TYR A 645 ARG 0.008 0.000 ARG A 96 *********************** 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 141 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7760 (ptp-110) cc_final: 0.7461 (ptp90) REVERT: B 407 MET cc_start: 0.6066 (tpt) cc_final: 0.5807 (mmm) REVERT: B 429 MET cc_start: 0.8025 (mpp) cc_final: 0.7093 (tpt) REVERT: B 442 MET cc_start: 0.7722 (ptp) cc_final: 0.6946 (tpt) REVERT: B 664 THR cc_start: 0.8658 (t) cc_final: 0.8346 (p) REVERT: B 720 MET cc_start: 0.8575 (ppp) cc_final: 0.7991 (ppp) REVERT: B 803 CYS cc_start: 0.8823 (m) cc_final: 0.8575 (m) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2182 time to fit residues: 47.3849 Evaluate side-chains 110 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 267 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.117442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.097464 restraints weight = 37886.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.096784 restraints weight = 40824.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.097424 restraints weight = 39066.143| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12599 Z= 0.229 Angle : 0.651 9.523 17065 Z= 0.332 Chirality : 0.044 0.209 1915 Planarity : 0.004 0.047 2147 Dihedral : 5.802 70.785 1754 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.48 % Favored : 90.39 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -1.47 (0.21), residues: 1550 helix: 0.62 (0.20), residues: 638 sheet: -2.69 (0.46), residues: 116 loop : -2.12 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 532 HIS 0.005 0.001 HIS B 267 PHE 0.027 0.002 PHE A 112 TYR 0.023 0.001 TYR A 209 ARG 0.008 0.000 ARG A 96 ********************** 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 145 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8628 (tpp) cc_final: 0.8383 (tpp) REVERT: A 96 ARG cc_start: 0.7646 (ptp-110) cc_final: 0.7281 (ptp90) REVERT: A 429 MET cc_start: 0.8642 (mpp) cc_final: 0.8428 (mpp) REVERT: A 477 ASP cc_start: 0.8166 (m-30) cc_final: 0.7717 (m-30) REVERT: B 429 MET cc_start: 0.8056 (mpp) cc_final: 0.7125 (tpt) REVERT: B 442 MET cc_start: 0.7706 (ptp) cc_final: 0.6856 (tpt) REVERT: B 524 ARG cc_start: 0.6139 (mmp-170) cc_final: 0.5826 (mmp-170) REVERT: B 720 MET cc_start: 0.8636 (ppp) cc_final: 0.8058 (ppp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2135 time to fit residues: 47.5989 Evaluate side-chains 114 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 119 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 140 optimal weight: 0.0970 chunk 54 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 267 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.119460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.098456 restraints weight = 37080.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.098131 restraints weight = 35055.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.098823 restraints weight = 32241.981| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 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 : 0.003 0.050 12599 Z= 0.180 Angle : 0.639 8.806 17065 Z= 0.322 Chirality : 0.044 0.197 1915 Planarity : 0.004 0.046 2147 Dihedral : 5.636 69.937 1754 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.84 % Favored : 91.03 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -1.32 (0.21), residues: 1550 helix: 0.77 (0.20), residues: 643 sheet: -2.69 (0.50), residues: 101 loop : -2.10 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 532 HIS 0.004 0.001 HIS B 267 PHE 0.027 0.002 PHE A 112 TYR 0.011 0.001 TYR A 779 ARG 0.007 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3087.51 seconds wall clock time: 57 minutes 28.48 seconds (3448.48 seconds total)