Starting phenix.real_space_refine on Tue Jul 29 20:51:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fd9_31537/07_2025/7fd9_31537.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fd9_31537/07_2025/7fd9_31537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fd9_31537/07_2025/7fd9_31537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fd9_31537/07_2025/7fd9_31537.map" model { file = "/net/cci-nas-00/data/ceres_data/7fd9_31537/07_2025/7fd9_31537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fd9_31537/07_2025/7fd9_31537.cif" } resolution = 4.0 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= 0.002 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 110 5.16 5 C 7384 2.51 5 N 1916 2.21 5 O 2066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5698 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 32, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 194 Chain: "B" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5698 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 32, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 194 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 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: 7.70, per 1000 atoms: 0.67 Number of scatterers: 11476 At special positions: 0 Unit cell: (79.21, 112.14, 178.89, 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 110 16.00 O 2066 8.00 N 1916 7.00 C 7384 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=2.02 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.05 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.05 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.04 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=2.04 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=2.04 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: 3.16 Conformation dependent library (CDL) restraints added in 1.7 seconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 51.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.664A pdb=" N VAL A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.570A pdb=" N SER A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 removed outlier: 4.419A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.514A pdb=" N LEU A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 210 removed outlier: 3.632A pdb=" N GLN A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.588A pdb=" N GLU A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.750A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.509A pdb=" N GLN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.564A pdb=" N MET A 429 " --> pdb=" O CYS A 426 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 430' Processing helix chain 'A' and resid 433 through 443 Processing helix chain 'A' and resid 496 through 499 Processing helix chain 'A' and resid 577 through 604 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 617 through 636 removed outlier: 3.533A pdb=" N ILE A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 673 removed outlier: 3.914A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 692 through 715 removed outlier: 3.692A pdb=" N ILE A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 760 Proline residue: A 743 - end of helix removed outlier: 3.985A pdb=" N LYS A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 770 Processing helix chain 'A' and resid 770 through 794 Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 797 through 818 Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.664A pdb=" N VAL B 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.571A pdb=" N SER B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 163 removed outlier: 4.419A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.515A pdb=" N LEU B 179 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.631A pdb=" N GLN B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.588A pdb=" N GLU B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.750A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.509A pdb=" N GLN B 360 " --> pdb=" O GLN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 419 Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.564A pdb=" N MET B 429 " --> pdb=" O CYS B 426 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 430 " --> pdb=" O ASP B 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 426 through 430' Processing helix chain 'B' and resid 433 through 443 Processing helix chain 'B' and resid 496 through 499 Processing helix chain 'B' and resid 577 through 604 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 636 removed outlier: 3.533A pdb=" N ILE B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 673 removed outlier: 3.913A pdb=" N ARG B 648 " --> pdb=" O CYS B 644 " (cutoff:3.500A) Proline residue: B 655 - end of helix Processing helix chain 'B' and resid 692 through 715 removed outlier: 3.693A pdb=" N ILE B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 760 Proline residue: B 743 - end of helix removed outlier: 3.986A pdb=" N LYS B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 770 Processing helix chain 'B' and resid 770 through 794 Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 797 through 818 Processing helix chain 'B' and resid 818 through 826 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.788A pdb=" N GLU A 94 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 96 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 41 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE A 36 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 146 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 38 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 248 removed outlier: 8.075A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N HIS A 218 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TYR A 213 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ALA A 275 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE A 277 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL A 217 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 329 removed outlier: 6.818A pdb=" N TYR A 466 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER A 486 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE A 468 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.838A pdb=" N PHE A 446 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 521 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 558 Processing sheet with id=AA7, first strand: chain 'A' and resid 720 through 722 Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.789A pdb=" N GLU B 94 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 96 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 41 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 36 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 146 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY B 38 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 241 through 248 removed outlier: 8.076A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYR B 213 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ALA B 275 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE B 277 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL B 217 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 329 removed outlier: 6.819A pdb=" N TYR B 466 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER B 486 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE B 468 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 445 through 447 removed outlier: 3.838A pdb=" N PHE B 446 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AB4, first strand: chain 'B' and resid 556 through 558 Processing sheet with id=AB5, first strand: chain 'B' and resid 720 through 722 596 hydrogen bonds defined for protein. 1722 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: 3.75 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3604 1.34 - 1.47: 2964 1.47 - 1.59: 5018 1.59 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 11742 Sorted by residual: bond pdb=" CAS Z99 A 902 " pdb=" CAU Z99 A 902 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" CAS Z99 B 902 " pdb=" CAU Z99 B 902 " ideal model delta sigma weight residual 1.390 1.479 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" CAT Z99 A 902 " pdb=" CAV Z99 A 902 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" CAT Z99 B 902 " pdb=" CAV Z99 B 902 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C CYS B 419 " pdb=" N PRO B 420 " ideal model delta sigma weight residual 1.331 1.358 -0.026 7.90e-03 1.60e+04 1.10e+01 ... (remaining 11737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 15951 4.37 - 8.74: 37 8.74 - 13.11: 12 13.11 - 17.49: 2 17.49 - 21.86: 2 Bond angle restraints: 16004 Sorted by residual: angle pdb=" CAN Z99 A 902 " pdb=" CAW Z99 A 902 " pdb=" CAV Z99 A 902 " ideal model delta sigma weight residual 108.20 130.06 -21.86 3.00e+00 1.11e-01 5.31e+01 angle pdb=" CAN Z99 B 902 " pdb=" CAW Z99 B 902 " pdb=" CAV Z99 B 902 " ideal model delta sigma weight residual 108.20 130.05 -21.85 3.00e+00 1.11e-01 5.30e+01 angle pdb=" CAW Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAY Z99 B 902 " ideal model delta sigma weight residual 117.71 131.39 -13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CAW Z99 A 902 " pdb=" CAN Z99 A 902 " pdb=" CAY Z99 A 902 " ideal model delta sigma weight residual 117.71 131.35 -13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" CAT Z99 A 902 " pdb=" CAV Z99 A 902 " pdb=" CAW Z99 A 902 " ideal model delta sigma weight residual 118.77 106.06 12.71 3.00e+00 1.11e-01 1.80e+01 ... (remaining 15999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 6886 34.06 - 68.11: 102 68.11 - 102.17: 22 102.17 - 136.23: 6 136.23 - 170.28: 18 Dihedral angle restraints: 7034 sinusoidal: 2574 harmonic: 4460 Sorted by residual: dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -164.80 78.80 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 530 " pdb=" CB CYS B 530 " ideal model delta sinusoidal sigma weight residual -86.00 -164.77 78.77 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 549 " pdb=" CB CYS B 549 " ideal model delta sinusoidal sigma weight residual 93.00 155.70 -62.70 1 1.00e+01 1.00e-02 5.20e+01 ... (remaining 7031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.536: 1844 0.536 - 1.072: 2 1.072 - 1.607: 0 1.607 - 2.143: 0 2.143 - 2.679: 2 Chirality restraints: 1848 Sorted by residual: chirality pdb=" CAW Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAU Z99 B 902 " pdb=" CAV Z99 B 902 " both_signs ideal model delta sigma weight residual False 2.61 -0.07 2.68 2.00e-01 2.50e+01 1.79e+02 chirality pdb=" CAW Z99 A 902 " pdb=" CAN Z99 A 902 " pdb=" CAU Z99 A 902 " pdb=" CAV Z99 A 902 " both_signs ideal model delta sigma weight residual False 2.61 -0.06 2.67 2.00e-01 2.50e+01 1.79e+02 chirality pdb=" CAY Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAR Z99 B 902 " pdb=" CAZ Z99 B 902 " both_signs ideal model delta sigma weight residual False -2.97 -2.38 -0.59 2.00e-01 2.50e+01 8.66e+00 ... (remaining 1845 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAG Z99 A 902 " 0.016 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CAI Z99 A 902 " 0.008 2.00e-02 2.50e+03 pdb=" CAK Z99 A 902 " 0.006 2.00e-02 2.50e+03 pdb=" CAM Z99 A 902 " -0.023 2.00e-02 2.50e+03 pdb=" CAT Z99 A 902 " 0.002 2.00e-02 2.50e+03 pdb=" CAV Z99 A 902 " -0.035 2.00e-02 2.50e+03 pdb=" CAW Z99 A 902 " 0.043 2.00e-02 2.50e+03 pdb=" OAP Z99 A 902 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAG Z99 B 902 " 0.016 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CAI Z99 B 902 " 0.008 2.00e-02 2.50e+03 pdb=" CAK Z99 B 902 " 0.005 2.00e-02 2.50e+03 pdb=" CAM Z99 B 902 " -0.022 2.00e-02 2.50e+03 pdb=" CAT Z99 B 902 " 0.003 2.00e-02 2.50e+03 pdb=" CAV Z99 B 902 " -0.034 2.00e-02 2.50e+03 pdb=" CAW Z99 B 902 " 0.042 2.00e-02 2.50e+03 pdb=" OAP Z99 B 902 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAF Z99 A 902 " 0.000 2.00e-02 2.50e+03 1.22e-02 3.00e+00 pdb=" CAH Z99 A 902 " 0.000 2.00e-02 2.50e+03 pdb=" CAJ Z99 A 902 " 0.000 2.00e-02 2.50e+03 pdb=" CAL Z99 A 902 " 0.011 2.00e-02 2.50e+03 pdb=" CAS Z99 A 902 " 0.007 2.00e-02 2.50e+03 pdb=" CAU Z99 A 902 " -0.030 2.00e-02 2.50e+03 pdb=" CAW Z99 A 902 " 0.011 2.00e-02 2.50e+03 pdb=" OAP Z99 A 902 " 0.001 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1877 2.79 - 3.32: 12074 3.32 - 3.85: 19082 3.85 - 4.37: 20764 4.37 - 4.90: 35950 Nonbonded interactions: 89747 Sorted by model distance: nonbonded pdb=" OE1 GLN A 198 " pdb=" OG SER A 304 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLN B 198 " pdb=" OG SER B 304 " model vdw 2.266 3.040 nonbonded pdb=" O SER A 116 " pdb=" OG SER A 119 " model vdw 2.288 3.040 nonbonded pdb=" O SER B 116 " pdb=" OG SER B 119 " model vdw 2.288 3.040 nonbonded pdb=" NH2 ARG B 648 " pdb=" OD1 ASN B 734 " model vdw 2.320 3.120 ... (remaining 89742 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.860 Find NCS groups from input model: 0.380 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 11764 Z= 0.464 Angle : 1.313 21.858 16050 Z= 0.844 Chirality : 0.127 2.679 1848 Planarity : 0.003 0.023 2026 Dihedral : 17.544 170.285 4110 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1522 helix: 0.96 (0.19), residues: 700 sheet: -0.60 (0.47), residues: 124 loop : -2.22 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 532 HIS 0.004 0.002 HIS B 53 PHE 0.013 0.003 PHE B 165 TYR 0.012 0.002 TYR A 645 ARG 0.006 0.001 ARG B 351 Details of bonding type rmsd link_NAG-ASN : bond 0.02961 ( 2) link_NAG-ASN : angle 14.36925 ( 6) hydrogen bonds : bond 0.12546 ( 596) hydrogen bonds : angle 5.66462 ( 1722) SS BOND : bond 0.00751 ( 20) SS BOND : angle 1.44731 ( 40) covalent geometry : bond 0.00703 (11742) covalent geometry : angle 1.28268 (16004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 414 MET cc_start: 0.8629 (tmm) cc_final: 0.8350 (tmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1777 time to fit residues: 22.3596 Evaluate side-chains 60 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 74 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.071039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.050014 restraints weight = 70867.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.051281 restraints weight = 36754.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.052143 restraints weight = 23873.217| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11764 Z= 0.156 Angle : 0.609 12.006 16050 Z= 0.301 Chirality : 0.043 0.220 1848 Planarity : 0.003 0.026 2026 Dihedral : 13.949 118.351 1742 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.80 % Allowed : 6.71 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.21), residues: 1522 helix: 1.23 (0.19), residues: 724 sheet: -0.75 (0.43), residues: 138 loop : -1.95 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 500 HIS 0.004 0.001 HIS A 361 PHE 0.018 0.001 PHE B 277 TYR 0.022 0.001 TYR A 340 ARG 0.002 0.000 ARG B 200 Details of bonding type rmsd link_NAG-ASN : bond 0.01682 ( 2) link_NAG-ASN : angle 8.17078 ( 6) hydrogen bonds : bond 0.04482 ( 596) hydrogen bonds : angle 4.61304 ( 1722) SS BOND : bond 0.00284 ( 20) SS BOND : angle 0.90665 ( 40) covalent geometry : bond 0.00335 (11742) covalent geometry : angle 0.58695 (16004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.9031 (tmm) cc_final: 0.8684 (tmm) REVERT: B 290 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8140 (mmm) REVERT: B 414 MET cc_start: 0.9080 (tmm) cc_final: 0.8585 (tmm) outliers start: 9 outliers final: 0 residues processed: 67 average time/residue: 0.1907 time to fit residues: 21.2564 Evaluate side-chains 62 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 30.0000 chunk 130 optimal weight: 40.0000 chunk 109 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.070564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.049291 restraints weight = 71724.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.050586 restraints weight = 37275.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.051458 restraints weight = 24311.470| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 : 0.004 0.050 11764 Z= 0.170 Angle : 0.578 11.941 16050 Z= 0.287 Chirality : 0.043 0.239 1848 Planarity : 0.003 0.028 2026 Dihedral : 10.220 124.208 1742 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.06 % Allowed : 8.13 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1522 helix: 1.36 (0.19), residues: 726 sheet: -0.74 (0.43), residues: 138 loop : -1.92 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 359 HIS 0.006 0.001 HIS B 74 PHE 0.015 0.001 PHE A 277 TYR 0.021 0.001 TYR B 340 ARG 0.003 0.000 ARG B 200 Details of bonding type rmsd link_NAG-ASN : bond 0.01711 ( 2) link_NAG-ASN : angle 7.58769 ( 6) hydrogen bonds : bond 0.03965 ( 596) hydrogen bonds : angle 4.37774 ( 1722) SS BOND : bond 0.00700 ( 20) SS BOND : angle 0.88962 ( 40) covalent geometry : bond 0.00361 (11742) covalent geometry : angle 0.55797 (16004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: B 277 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8369 (m-80) REVERT: B 290 MET cc_start: 0.8482 (mmp) cc_final: 0.8150 (mmm) REVERT: B 414 MET cc_start: 0.9044 (tmm) cc_final: 0.8530 (tmm) outliers start: 12 outliers final: 3 residues processed: 69 average time/residue: 0.2051 time to fit residues: 23.1395 Evaluate side-chains 63 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 78 optimal weight: 0.0980 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 88 ASN ** B 159 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 = 0.3707 r_free = 0.3707 target = 0.070761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.051055 restraints weight = 73930.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.051367 restraints weight = 44899.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.051921 restraints weight = 30850.258| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11764 Z= 0.209 Angle : 0.595 11.503 16050 Z= 0.298 Chirality : 0.043 0.219 1848 Planarity : 0.003 0.029 2026 Dihedral : 9.300 133.578 1742 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.59 % Allowed : 9.01 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1522 helix: 1.38 (0.19), residues: 728 sheet: -0.65 (0.44), residues: 138 loop : -1.84 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 359 HIS 0.004 0.001 HIS A 361 PHE 0.014 0.001 PHE B 277 TYR 0.027 0.001 TYR A 340 ARG 0.003 0.000 ARG B 26 Details of bonding type rmsd link_NAG-ASN : bond 0.01796 ( 2) link_NAG-ASN : angle 7.20944 ( 6) hydrogen bonds : bond 0.03897 ( 596) hydrogen bonds : angle 4.39765 ( 1722) SS BOND : bond 0.00271 ( 20) SS BOND : angle 0.98940 ( 40) covalent geometry : bond 0.00446 (11742) covalent geometry : angle 0.57711 (16004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: A 414 MET cc_start: 0.9158 (tmm) cc_final: 0.8780 (tmm) REVERT: B 277 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: B 290 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8260 (mmm) REVERT: B 414 MET cc_start: 0.9125 (tmm) cc_final: 0.8878 (tmm) outliers start: 18 outliers final: 6 residues processed: 72 average time/residue: 0.2167 time to fit residues: 25.9254 Evaluate side-chains 67 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 50.0000 chunk 57 optimal weight: 0.0170 chunk 149 optimal weight: 9.9990 chunk 147 optimal weight: 50.0000 chunk 140 optimal weight: 40.0000 chunk 79 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 93 optimal weight: 0.3980 overall best weight: 1.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.070688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.049133 restraints weight = 70556.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.050428 restraints weight = 36833.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.051339 restraints weight = 24000.742| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11764 Z= 0.122 Angle : 0.543 11.239 16050 Z= 0.269 Chirality : 0.041 0.192 1848 Planarity : 0.003 0.030 2026 Dihedral : 9.086 134.246 1742 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.50 % Allowed : 9.28 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1522 helix: 1.45 (0.19), residues: 732 sheet: -0.56 (0.44), residues: 138 loop : -1.81 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 500 HIS 0.003 0.001 HIS A 361 PHE 0.010 0.001 PHE A 277 TYR 0.014 0.001 TYR A 340 ARG 0.003 0.000 ARG B 200 Details of bonding type rmsd link_NAG-ASN : bond 0.01671 ( 2) link_NAG-ASN : angle 7.09861 ( 6) hydrogen bonds : bond 0.03691 ( 596) hydrogen bonds : angle 4.23065 ( 1722) SS BOND : bond 0.00164 ( 20) SS BOND : angle 0.81852 ( 40) covalent geometry : bond 0.00260 (11742) covalent geometry : angle 0.52480 (16004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 1.857 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: A 414 MET cc_start: 0.9035 (tmm) cc_final: 0.8777 (tmm) REVERT: B 277 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: B 290 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8180 (mmm) REVERT: B 405 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: B 414 MET cc_start: 0.9131 (tmm) cc_final: 0.8878 (tmm) outliers start: 17 outliers final: 8 residues processed: 73 average time/residue: 0.2615 time to fit residues: 31.4452 Evaluate side-chains 72 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 150 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.069018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.047487 restraints weight = 70105.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.048713 restraints weight = 36610.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.049520 restraints weight = 24010.468| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11764 Z= 0.268 Angle : 0.651 10.455 16050 Z= 0.324 Chirality : 0.044 0.198 1848 Planarity : 0.003 0.029 2026 Dihedral : 9.103 136.144 1742 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.86 % Allowed : 9.81 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1522 helix: 1.32 (0.19), residues: 732 sheet: -0.57 (0.45), residues: 138 loop : -1.81 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 359 HIS 0.005 0.001 HIS A 361 PHE 0.012 0.001 PHE A 277 TYR 0.022 0.001 TYR A 340 ARG 0.003 0.000 ARG A 26 Details of bonding type rmsd link_NAG-ASN : bond 0.01229 ( 2) link_NAG-ASN : angle 6.96316 ( 6) hydrogen bonds : bond 0.03959 ( 596) hydrogen bonds : angle 4.44407 ( 1722) SS BOND : bond 0.00253 ( 20) SS BOND : angle 0.94599 ( 40) covalent geometry : bond 0.00571 (11742) covalent geometry : angle 0.63653 (16004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: A 405 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: B 277 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: B 290 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8214 (mmm) REVERT: B 405 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8067 (m-10) outliers start: 21 outliers final: 9 residues processed: 73 average time/residue: 0.1999 time to fit residues: 24.0041 Evaluate side-chains 72 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 54 optimal weight: 50.0000 chunk 53 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.069243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.047497 restraints weight = 70617.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.048855 restraints weight = 37001.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.049705 restraints weight = 24142.193| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11764 Z= 0.227 Angle : 0.626 10.372 16050 Z= 0.309 Chirality : 0.042 0.143 1848 Planarity : 0.003 0.029 2026 Dihedral : 9.127 136.551 1742 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.03 % Allowed : 10.16 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1522 helix: 1.34 (0.19), residues: 720 sheet: -0.70 (0.43), residues: 148 loop : -1.85 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 557 HIS 0.005 0.001 HIS A 361 PHE 0.010 0.001 PHE B 363 TYR 0.018 0.001 TYR B 340 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.01200 ( 2) link_NAG-ASN : angle 6.79316 ( 6) hydrogen bonds : bond 0.03890 ( 596) hydrogen bonds : angle 4.38265 ( 1722) SS BOND : bond 0.00227 ( 20) SS BOND : angle 0.85926 ( 40) covalent geometry : bond 0.00486 (11742) covalent geometry : angle 0.61192 (16004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: A 405 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7953 (m-10) REVERT: B 277 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: B 290 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8197 (mmm) REVERT: B 405 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.8036 (m-80) outliers start: 23 outliers final: 11 residues processed: 76 average time/residue: 0.2161 time to fit residues: 26.0938 Evaluate side-chains 74 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 73 optimal weight: 0.0980 chunk 97 optimal weight: 6.9990 chunk 63 optimal weight: 40.0000 chunk 85 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.069621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.047872 restraints weight = 70708.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049159 restraints weight = 36877.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.050025 restraints weight = 24012.314| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11764 Z= 0.167 Angle : 0.598 11.016 16050 Z= 0.292 Chirality : 0.041 0.140 1848 Planarity : 0.003 0.029 2026 Dihedral : 9.025 136.635 1742 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.59 % Allowed : 11.13 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1522 helix: 1.34 (0.19), residues: 732 sheet: -0.49 (0.44), residues: 138 loop : -1.82 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 557 HIS 0.004 0.001 HIS A 361 PHE 0.008 0.001 PHE B 363 TYR 0.016 0.001 TYR B 340 ARG 0.002 0.000 ARG B 26 Details of bonding type rmsd link_NAG-ASN : bond 0.01253 ( 2) link_NAG-ASN : angle 6.59808 ( 6) hydrogen bonds : bond 0.03790 ( 596) hydrogen bonds : angle 4.28904 ( 1722) SS BOND : bond 0.00188 ( 20) SS BOND : angle 0.79957 ( 40) covalent geometry : bond 0.00361 (11742) covalent geometry : angle 0.58379 (16004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 1.524 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.8695 (tpp) cc_final: 0.8226 (mmp) REVERT: A 277 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: A 405 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: B 277 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: B 290 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8196 (mmm) REVERT: B 405 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7906 (m-10) REVERT: B 414 MET cc_start: 0.9064 (tmm) cc_final: 0.8425 (tmm) REVERT: B 429 MET cc_start: 0.8212 (ttm) cc_final: 0.7950 (tpp) outliers start: 18 outliers final: 13 residues processed: 74 average time/residue: 0.2524 time to fit residues: 29.3007 Evaluate side-chains 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 6.9990 chunk 49 optimal weight: 40.0000 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 134 optimal weight: 40.0000 chunk 24 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 112 optimal weight: 8.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.069689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.048062 restraints weight = 70849.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.049338 restraints weight = 36586.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.050151 restraints weight = 23924.494| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11764 Z= 0.170 Angle : 0.613 11.965 16050 Z= 0.297 Chirality : 0.041 0.135 1848 Planarity : 0.003 0.029 2026 Dihedral : 8.961 137.063 1742 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.03 % Allowed : 10.87 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1522 helix: 1.41 (0.19), residues: 730 sheet: -0.42 (0.45), residues: 138 loop : -1.79 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 557 HIS 0.004 0.001 HIS A 361 PHE 0.008 0.001 PHE B 363 TYR 0.015 0.001 TYR B 340 ARG 0.002 0.000 ARG B 26 Details of bonding type rmsd link_NAG-ASN : bond 0.01142 ( 2) link_NAG-ASN : angle 6.45329 ( 6) hydrogen bonds : bond 0.03738 ( 596) hydrogen bonds : angle 4.27916 ( 1722) SS BOND : bond 0.00188 ( 20) SS BOND : angle 0.81721 ( 40) covalent geometry : bond 0.00366 (11742) covalent geometry : angle 0.59956 (16004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: A 405 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: B 277 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: B 290 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8190 (mmm) REVERT: B 405 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.7894 (m-10) REVERT: B 414 MET cc_start: 0.9087 (tmm) cc_final: 0.8674 (tmm) outliers start: 23 outliers final: 15 residues processed: 80 average time/residue: 0.2113 time to fit residues: 26.5748 Evaluate side-chains 80 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 0.0370 chunk 22 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.070393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.048868 restraints weight = 69967.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.050142 restraints weight = 36260.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.050964 restraints weight = 23732.675| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11764 Z= 0.113 Angle : 0.588 12.998 16050 Z= 0.281 Chirality : 0.041 0.145 1848 Planarity : 0.003 0.030 2026 Dihedral : 8.789 136.880 1742 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.86 % Allowed : 10.95 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1522 helix: 1.57 (0.19), residues: 724 sheet: -0.40 (0.44), residues: 138 loop : -1.69 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 557 HIS 0.002 0.001 HIS A 74 PHE 0.007 0.001 PHE B 165 TYR 0.013 0.001 TYR B 340 ARG 0.001 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.01351 ( 2) link_NAG-ASN : angle 6.32039 ( 6) hydrogen bonds : bond 0.03607 ( 596) hydrogen bonds : angle 4.17555 ( 1722) SS BOND : bond 0.00153 ( 20) SS BOND : angle 0.79826 ( 40) covalent geometry : bond 0.00245 (11742) covalent geometry : angle 0.57461 (16004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: B 228 MET cc_start: 0.8570 (tpp) cc_final: 0.8069 (mmp) REVERT: B 290 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8196 (mmm) REVERT: B 405 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7807 (m-10) REVERT: B 414 MET cc_start: 0.8906 (tmm) cc_final: 0.8678 (tmm) REVERT: B 429 MET cc_start: 0.8541 (tpp) cc_final: 0.8188 (tpp) outliers start: 21 outliers final: 14 residues processed: 77 average time/residue: 0.2921 time to fit residues: 34.3156 Evaluate side-chains 79 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 0.0000 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.070776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.049279 restraints weight = 70186.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050570 restraints weight = 36170.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051420 restraints weight = 23606.417| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11764 Z= 0.106 Angle : 0.589 12.178 16050 Z= 0.280 Chirality : 0.040 0.136 1848 Planarity : 0.003 0.031 2026 Dihedral : 8.491 137.414 1742 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.59 % Allowed : 11.48 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1522 helix: 1.70 (0.19), residues: 726 sheet: -0.28 (0.43), residues: 138 loop : -1.65 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 557 HIS 0.002 0.001 HIS A 101 PHE 0.007 0.001 PHE B 165 TYR 0.012 0.001 TYR B 340 ARG 0.003 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.01299 ( 2) link_NAG-ASN : angle 5.77667 ( 6) hydrogen bonds : bond 0.03474 ( 596) hydrogen bonds : angle 4.10471 ( 1722) SS BOND : bond 0.00143 ( 20) SS BOND : angle 0.81283 ( 40) covalent geometry : bond 0.00230 (11742) covalent geometry : angle 0.57759 (16004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3833.16 seconds wall clock time: 71 minutes 20.44 seconds (4280.44 seconds total)