Starting phenix.real_space_refine on Thu Sep 26 01:00:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/09_2024/7fd9_31537.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/09_2024/7fd9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/09_2024/7fd9_31537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/09_2024/7fd9_31537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/09_2024/7fd9_31537.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/09_2024/7fd9_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.88, per 1000 atoms: 0.60 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: 2.84 Conformation dependent library (CDL) restraints added in 1.6 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: 1.30 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: 3.49 Time building geometry restraints manager: 3.29 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: 0.00 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: 2.270 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.630 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.460 ------------------------------------------------------------------------------- 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 11742 Z= 0.455 Angle : 1.283 21.858 16004 Z= 0.839 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.390 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: 0.1925 time to fit residues: 24.1230 Evaluate side-chains 60 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 11742 Z= 0.223 Angle : 0.587 9.019 16004 Z= 0.296 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8459 (tmm) cc_final: 0.8199 (tmm) REVERT: B 290 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7968 (mmm) REVERT: B 414 MET cc_start: 0.8560 (tmm) cc_final: 0.8189 (tmm) outliers start: 9 outliers final: 0 residues processed: 67 average time/residue: 0.1982 time to fit residues: 22.4805 Evaluate side-chains 62 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 76 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 0.0970 chunk 93 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 50.0000 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 overall best weight: 5.6186 ------------------------------------------------------------------------------- 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** B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11742 Z= 0.400 Angle : 0.658 6.820 16004 Z= 0.334 Chirality : 0.045 0.254 1848 Planarity : 0.004 0.028 2026 Dihedral : 10.380 125.602 1742 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.24 % Allowed : 8.66 % Favored : 90.11 % 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: -0.57 (0.21), residues: 1522 helix: 1.15 (0.19), residues: 720 sheet: -0.88 (0.42), residues: 138 loop : -2.05 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 359 HIS 0.005 0.002 HIS A 361 PHE 0.018 0.001 PHE A 277 TYR 0.027 0.002 TYR B 340 ARG 0.005 0.001 ARG B 200 *********************** 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 fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8389 (ttp) REVERT: A 277 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: B 277 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8202 (m-80) REVERT: B 290 MET cc_start: 0.8316 (mmp) cc_final: 0.7925 (mmm) outliers start: 14 outliers final: 3 residues processed: 67 average time/residue: 0.1891 time to fit residues: 20.7123 Evaluate side-chains 64 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 72 MET 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 136 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 40.0000 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 40.0000 chunk 39 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11742 Z= 0.303 Angle : 0.578 8.351 16004 Z= 0.295 Chirality : 0.043 0.230 1848 Planarity : 0.003 0.029 2026 Dihedral : 9.526 132.077 1742 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.03 % Allowed : 9.01 % Favored : 88.96 % 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: -0.38 (0.21), residues: 1522 helix: 1.21 (0.19), residues: 732 sheet: -0.78 (0.44), residues: 138 loop : -1.90 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 359 HIS 0.005 0.001 HIS A 74 PHE 0.013 0.001 PHE A 277 TYR 0.023 0.001 TYR B 340 ARG 0.002 0.000 ARG B 26 *********************** 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 85 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.8619 (tmm) cc_final: 0.8252 (tmm) REVERT: B 290 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7964 (mmm) REVERT: B 405 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7557 (m-10) REVERT: B 414 MET cc_start: 0.8472 (tmm) cc_final: 0.8205 (tmm) outliers start: 23 outliers final: 8 residues processed: 78 average time/residue: 0.2002 time to fit residues: 25.6339 Evaluate side-chains 71 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 286 LEU 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 290 MET Chi-restraints excluded: chain B residue 405 TYR 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 122 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 chunk 101 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 131 optimal weight: 40.0000 chunk 37 optimal weight: 0.7980 overall best weight: 7.1590 ------------------------------------------------------------------------------- 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 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11742 Z= 0.479 Angle : 0.689 8.144 16004 Z= 0.352 Chirality : 0.045 0.209 1848 Planarity : 0.004 0.029 2026 Dihedral : 9.435 134.798 1742 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % 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: -0.57 (0.21), residues: 1522 helix: 1.07 (0.19), residues: 720 sheet: -1.01 (0.43), residues: 148 loop : -1.92 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 500 HIS 0.006 0.002 HIS A 361 PHE 0.013 0.002 PHE B 363 TYR 0.028 0.002 TYR A 340 ARG 0.003 0.000 ARG B 26 *********************** 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 82 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 59 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: B 290 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7982 (mmm) REVERT: B 405 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7838 (m-80) outliers start: 23 outliers final: 14 residues processed: 76 average time/residue: 0.2189 time to fit residues: 25.8085 Evaluate side-chains 74 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 57 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 444 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 147 optimal weight: 30.0000 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 30.0000 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11742 Z= 0.190 Angle : 0.553 8.962 16004 Z= 0.278 Chirality : 0.042 0.238 1848 Planarity : 0.003 0.030 2026 Dihedral : 9.208 134.696 1742 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.94 % Allowed : 10.78 % 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: -0.24 (0.21), residues: 1522 helix: 1.33 (0.19), residues: 732 sheet: -0.72 (0.44), residues: 138 loop : -1.82 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 500 HIS 0.004 0.001 HIS A 361 PHE 0.009 0.001 PHE B 165 TYR 0.015 0.001 TYR B 340 ARG 0.002 0.000 ARG B 26 *********************** 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 82 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7391 (m-10) REVERT: B 290 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.8003 (mmm) REVERT: B 405 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7466 (m-10) outliers start: 22 outliers final: 11 residues processed: 74 average time/residue: 0.1957 time to fit residues: 23.9195 Evaluate side-chains 73 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 203 VAL 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 141 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11742 Z= 0.290 Angle : 0.597 9.963 16004 Z= 0.299 Chirality : 0.042 0.211 1848 Planarity : 0.003 0.029 2026 Dihedral : 9.125 135.555 1742 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.21 % Allowed : 10.25 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1522 helix: 1.34 (0.19), residues: 720 sheet: -0.73 (0.43), residues: 148 loop : -1.83 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 557 HIS 0.004 0.001 HIS A 361 PHE 0.009 0.001 PHE B 363 TYR 0.018 0.001 TYR A 340 ARG 0.002 0.000 ARG B 26 *********************** 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 85 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 60 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: B 290 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8024 (mmm) REVERT: B 405 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7566 (m-10) outliers start: 25 outliers final: 18 residues processed: 78 average time/residue: 0.2059 time to fit residues: 25.4171 Evaluate side-chains 79 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 58 time to evaluate : 1.557 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 444 THR 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 106 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 234 MET 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 58 optimal weight: 30.0000 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 40.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11742 Z= 0.237 Angle : 0.579 10.459 16004 Z= 0.287 Chirality : 0.042 0.202 1848 Planarity : 0.003 0.029 2026 Dihedral : 9.028 136.010 1742 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.30 % Allowed : 11.04 % Favored : 86.66 % 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: -0.21 (0.22), residues: 1522 helix: 1.39 (0.19), residues: 720 sheet: -0.68 (0.43), residues: 148 loop : -1.81 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 A 26 *********************** 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 86 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 60 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: B 290 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8003 (mmm) REVERT: B 405 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: B 414 MET cc_start: 0.8540 (tmm) cc_final: 0.8126 (tmm) outliers start: 26 outliers final: 18 residues processed: 79 average time/residue: 0.2182 time to fit residues: 27.2437 Evaluate side-chains 80 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 VAL 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 106 LEU Chi-restraints excluded: chain B residue 203 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 663 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 128 optimal weight: 40.0000 chunk 136 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 11742 Z= 0.449 Angle : 0.712 11.400 16004 Z= 0.355 Chirality : 0.044 0.222 1848 Planarity : 0.004 0.028 2026 Dihedral : 9.214 137.637 1742 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.47 % Allowed : 11.04 % Favored : 86.48 % 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: -0.46 (0.22), residues: 1522 helix: 1.10 (0.19), residues: 720 sheet: -0.84 (0.42), residues: 148 loop : -1.83 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 359 HIS 0.006 0.001 HIS A 361 PHE 0.012 0.001 PHE B 363 TYR 0.025 0.002 TYR A 340 ARG 0.004 0.001 ARG A 208 *********************** 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 86 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 58 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: B 290 MET cc_start: 0.8301 (mmp) cc_final: 0.7969 (mmm) REVERT: B 405 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7678 (m-10) outliers start: 28 outliers final: 19 residues processed: 80 average time/residue: 0.1908 time to fit residues: 24.3708 Evaluate side-chains 80 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 ILE 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 146 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 286 LEU 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 663 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 88 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 120 optimal weight: 0.0370 chunk 12 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 40.0000 overall best weight: 2.0664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11742 Z= 0.210 Angle : 0.602 12.025 16004 Z= 0.294 Chirality : 0.041 0.161 1848 Planarity : 0.003 0.029 2026 Dihedral : 9.077 136.837 1742 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.77 % Allowed : 11.75 % Favored : 86.48 % 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: -0.21 (0.22), residues: 1522 helix: 1.35 (0.19), residues: 720 sheet: -0.64 (0.43), residues: 148 loop : -1.78 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 487 HIS 0.003 0.001 HIS B 361 PHE 0.009 0.001 PHE A 277 TYR 0.015 0.001 TYR B 340 ARG 0.002 0.000 ARG A 208 ********************** 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 81 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 290 MET cc_start: 0.8455 (mmp) cc_final: 0.8211 (mmm) REVERT: A 405 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7421 (m-10) REVERT: B 290 MET cc_start: 0.8273 (mmp) cc_final: 0.7957 (mmm) REVERT: B 405 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7472 (m-10) REVERT: B 469 MET cc_start: 0.8047 (mmt) cc_final: 0.7635 (mmm) outliers start: 20 outliers final: 14 residues processed: 77 average time/residue: 0.2190 time to fit residues: 26.5314 Evaluate side-chains 76 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 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 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 203 VAL Chi-restraints excluded: chain B residue 286 LEU 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 663 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 36 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 50.0000 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 124 optimal weight: 0.0020 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 106 optimal weight: 0.0070 chunk 6 optimal weight: 7.9990 overall best weight: 0.7208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 641 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 = 0.3731 r_free = 0.3731 target = 0.070704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.049332 restraints weight = 70033.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.050592 restraints weight = 36246.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.051448 restraints weight = 23575.723| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11742 Z= 0.153 Angle : 0.583 12.494 16004 Z= 0.283 Chirality : 0.041 0.164 1848 Planarity : 0.003 0.030 2026 Dihedral : 8.733 136.782 1742 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.41 % Allowed : 12.01 % Favored : 86.57 % 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: 0.00 (0.22), residues: 1522 helix: 1.53 (0.19), residues: 730 sheet: -0.56 (0.43), residues: 148 loop : -1.72 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 487 HIS 0.002 0.000 HIS A 101 PHE 0.009 0.001 PHE B 446 TYR 0.012 0.001 TYR B 340 ARG 0.002 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.45 seconds wall clock time: 38 minutes 39.74 seconds (2319.74 seconds total)