Starting phenix.real_space_refine on Wed Feb 14 11:04:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/02_2024/6qpc_4613_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/02_2024/6qpc_4613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/02_2024/6qpc_4613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/02_2024/6qpc_4613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/02_2024/6qpc_4613_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/02_2024/6qpc_4613_updated.pdb" } resolution = 3.5 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= 0.010 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 62 5.16 5 C 6040 2.51 5 N 1454 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 250": "OD1" <-> "OD2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ASP 653": "OD1" <-> "OD2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 808": "NH1" <-> "NH2" Residue "A TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 810": "NH1" <-> "NH2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 250": "OD1" <-> "OD2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B GLU 548": "OE1" <-> "OE2" Residue "B TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B ASP 653": "OD1" <-> "OD2" Residue "B TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B ASP 749": "OD1" <-> "OD2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 808": "NH1" <-> "NH2" Residue "B TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 810": "NH1" <-> "NH2" Residue "B TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9140 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4530 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 28, 'TRANS': 548} Chain breaks: 10 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 126 Chain: "B" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4530 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 28, 'TRANS': 548} Chain breaks: 10 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 126 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'P1O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'P1O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.22, per 1000 atoms: 0.57 Number of scatterers: 9140 At special positions: 0 Unit cell: (94.116, 110.308, 109.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 62 16.00 P 2 15.00 O 1578 8.00 N 1454 7.00 C 6040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.02 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.04 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.02 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.7 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 0 sheets defined 64.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 236 through 239 No H-bonds generated for 'chain 'A' and resid 236 through 239' Processing helix chain 'A' and resid 265 through 272 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 294 through 329 removed outlier: 3.533A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASP A 329 " --> pdb=" O TYR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 361 through 374 removed outlier: 4.528A pdb=" N GLU A 366 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A 369 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A 370 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 removed outlier: 3.729A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 486 removed outlier: 3.667A pdb=" N ILE A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 538 Processing helix chain 'A' and resid 544 through 572 removed outlier: 4.855A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 636 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 686 through 709 Proline residue: A 689 - end of helix removed outlier: 3.543A pdb=" N VAL A 694 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE A 697 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 700 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 703 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 704 " --> pdb=" O ARG A 701 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 706 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 709 " --> pdb=" O LYS A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 745 removed outlier: 3.733A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 826 through 856 Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 294 through 329 removed outlier: 3.533A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASP B 329 " --> pdb=" O TYR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 361 through 374 removed outlier: 4.528A pdb=" N GLU B 366 " --> pdb=" O ILE B 363 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS B 369 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS B 370 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 403 removed outlier: 3.730A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 486 removed outlier: 3.666A pdb=" N ILE B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 538 Processing helix chain 'B' and resid 544 through 572 removed outlier: 4.854A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 636 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 649 through 654 Processing helix chain 'B' and resid 665 through 679 Processing helix chain 'B' and resid 686 through 709 Proline residue: B 689 - end of helix removed outlier: 3.542A pdb=" N VAL B 694 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 697 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE B 700 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 703 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 704 " --> pdb=" O ARG B 701 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 706 " --> pdb=" O ASP B 703 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 709 " --> pdb=" O LYS B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 745 removed outlier: 3.733A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 Processing helix chain 'B' and resid 776 through 780 Processing helix chain 'B' and resid 826 through 856 526 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1464 1.32 - 1.45: 2722 1.45 - 1.58: 5080 1.58 - 1.71: 6 1.71 - 1.83: 100 Bond restraints: 9372 Sorted by residual: bond pdb=" O3 P1O A1003 " pdb=" P1 P1O A1003 " ideal model delta sigma weight residual 1.648 1.770 -0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" O3 P1O B1003 " pdb=" P1 P1O B1003 " ideal model delta sigma weight residual 1.648 1.770 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C19 P1O A1003 " pdb=" C20 P1O A1003 " ideal model delta sigma weight residual 1.502 1.584 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C19 P1O B1003 " pdb=" C20 P1O B1003 " ideal model delta sigma weight residual 1.502 1.583 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C1 P1O B1003 " pdb=" C2 P1O B1003 " ideal model delta sigma weight residual 1.513 1.589 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 9367 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.58: 215 105.58 - 112.85: 4848 112.85 - 120.12: 3757 120.12 - 127.39: 3808 127.39 - 134.65: 106 Bond angle restraints: 12734 Sorted by residual: angle pdb=" CA TYR A 477 " pdb=" CB TYR A 477 " pdb=" CG TYR A 477 " ideal model delta sigma weight residual 113.90 122.44 -8.54 1.80e+00 3.09e-01 2.25e+01 angle pdb=" CA TYR B 477 " pdb=" CB TYR B 477 " pdb=" CG TYR B 477 " ideal model delta sigma weight residual 113.90 122.42 -8.52 1.80e+00 3.09e-01 2.24e+01 angle pdb=" C LEU B 503 " pdb=" N THR B 504 " pdb=" CA THR B 504 " ideal model delta sigma weight residual 121.62 128.96 -7.34 1.57e+00 4.06e-01 2.18e+01 angle pdb=" C LEU A 503 " pdb=" N THR A 504 " pdb=" CA THR A 504 " ideal model delta sigma weight residual 121.62 128.94 -7.32 1.57e+00 4.06e-01 2.17e+01 angle pdb=" C VAL A 484 " pdb=" N PHE A 485 " pdb=" CA PHE A 485 " ideal model delta sigma weight residual 120.29 113.76 6.53 1.42e+00 4.96e-01 2.11e+01 ... (remaining 12729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.87: 5251 27.87 - 55.73: 227 55.73 - 83.60: 18 83.60 - 111.47: 2 111.47 - 139.34: 2 Dihedral angle restraints: 5500 sinusoidal: 2100 harmonic: 3400 Sorted by residual: dihedral pdb=" CA ARG A 354 " pdb=" C ARG A 354 " pdb=" N LEU A 355 " pdb=" CA LEU A 355 " ideal model delta harmonic sigma weight residual -180.00 -131.65 -48.35 0 5.00e+00 4.00e-02 9.35e+01 dihedral pdb=" CA ARG B 354 " pdb=" C ARG B 354 " pdb=" N LEU B 355 " pdb=" CA LEU B 355 " ideal model delta harmonic sigma weight residual 180.00 -131.70 -48.30 0 5.00e+00 4.00e-02 9.33e+01 dihedral pdb=" CA CYS A 356 " pdb=" C CYS A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta harmonic sigma weight residual -180.00 -142.63 -37.37 0 5.00e+00 4.00e-02 5.59e+01 ... (remaining 5497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.016: 1424 1.016 - 2.032: 0 2.032 - 3.048: 0 3.048 - 4.064: 0 4.064 - 5.080: 2 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C7 P1O B1003 " pdb=" C6 P1O B1003 " pdb=" C8 P1O B1003 " pdb=" O7 P1O B1003 " both_signs ideal model delta sigma weight residual False -2.35 2.73 -5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" C7 P1O A1003 " pdb=" C6 P1O A1003 " pdb=" C8 P1O A1003 " pdb=" O7 P1O A1003 " both_signs ideal model delta sigma weight residual False -2.35 2.73 -5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" CB VAL A 531 " pdb=" CA VAL A 531 " pdb=" CG1 VAL A 531 " pdb=" CG2 VAL A 531 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 1423 not shown) Planarity restraints: 1564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 670 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C GLU A 670 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU A 670 " -0.019 2.00e-02 2.50e+03 pdb=" N MET A 671 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 670 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C GLU B 670 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU B 670 " 0.019 2.00e-02 2.50e+03 pdb=" N MET B 671 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 668 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C TYR A 668 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR A 668 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 669 " 0.017 2.00e-02 2.50e+03 ... (remaining 1561 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 524 2.72 - 3.27: 9503 3.27 - 3.81: 15827 3.81 - 4.36: 18262 4.36 - 4.90: 31164 Nonbonded interactions: 75280 Sorted by model distance: nonbonded pdb=" O VAL A 561 " pdb=" OG SER A 565 " model vdw 2.176 2.440 nonbonded pdb=" O VAL B 561 " pdb=" OG SER B 565 " model vdw 2.178 2.440 nonbonded pdb=" O ALA B 508 " pdb=" OG1 THR B 512 " model vdw 2.290 2.440 nonbonded pdb=" O ALA A 508 " pdb=" OG1 THR A 512 " model vdw 2.290 2.440 nonbonded pdb=" OG1 THR A 364 " pdb=" OG SER A 367 " model vdw 2.304 2.440 ... (remaining 75275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 4.150 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.440 Find NCS groups from input model: 0.530 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 0.009 0.122 9372 Z= 0.555 Angle : 1.011 11.295 12734 Z= 0.549 Chirality : 0.198 5.080 1426 Planarity : 0.009 0.069 1564 Dihedral : 15.204 139.337 3270 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.22 % Allowed : 6.06 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.19), residues: 1110 helix: -2.06 (0.14), residues: 760 sheet: None (None), residues: 0 loop : -2.19 (0.26), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 397 HIS 0.004 0.001 HIS A 830 PHE 0.032 0.003 PHE B 685 TYR 0.042 0.003 TYR B 580 ARG 0.004 0.001 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.8079 (tt0) cc_final: 0.7755 (tt0) REVERT: A 355 LEU cc_start: 0.5820 (tp) cc_final: 0.5102 (pt) REVERT: A 524 LEU cc_start: 0.8983 (tp) cc_final: 0.8671 (mt) REVERT: A 534 MET cc_start: 0.7100 (mtm) cc_final: 0.6763 (mtt) REVERT: A 650 TRP cc_start: 0.7373 (p90) cc_final: 0.6969 (p90) REVERT: A 695 ASN cc_start: 0.8817 (t0) cc_final: 0.8504 (t0) REVERT: A 730 GLN cc_start: 0.8584 (mt0) cc_final: 0.8269 (mm-40) REVERT: A 818 HIS cc_start: 0.6650 (t-90) cc_final: 0.6259 (t70) REVERT: B 294 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6223 (mm-30) REVERT: B 355 LEU cc_start: 0.5826 (tp) cc_final: 0.5268 (pt) REVERT: B 534 MET cc_start: 0.6973 (mtm) cc_final: 0.6652 (ptt) REVERT: B 650 TRP cc_start: 0.7392 (p90) cc_final: 0.6960 (p90) REVERT: B 661 LYS cc_start: 0.8480 (ptpt) cc_final: 0.8274 (mmmm) REVERT: B 730 GLN cc_start: 0.8561 (mt0) cc_final: 0.8262 (mm-40) outliers start: 2 outliers final: 2 residues processed: 216 average time/residue: 0.2054 time to fit residues: 61.3024 Evaluate side-chains 151 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 531 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.3980 chunk 86 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 695 ASN A 730 GLN B 608 GLN B 730 GLN B 818 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9372 Z= 0.199 Angle : 0.601 8.426 12734 Z= 0.321 Chirality : 0.039 0.150 1426 Planarity : 0.006 0.057 1564 Dihedral : 10.248 151.005 1308 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.31 % Allowed : 11.12 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.21), residues: 1110 helix: -0.46 (0.16), residues: 764 sheet: None (None), residues: 0 loop : -1.76 (0.27), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.008 0.001 HIS B 818 PHE 0.025 0.002 PHE B 485 TYR 0.030 0.002 TYR B 477 ARG 0.002 0.000 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.8052 (tt0) cc_final: 0.7645 (tt0) REVERT: A 650 TRP cc_start: 0.7365 (p90) cc_final: 0.7031 (p90) REVERT: A 730 GLN cc_start: 0.8527 (mt0) cc_final: 0.8301 (mm-40) REVERT: B 265 GLU cc_start: 0.8066 (tt0) cc_final: 0.7629 (tt0) REVERT: B 267 TYR cc_start: 0.7082 (t80) cc_final: 0.6846 (t80) REVERT: B 650 TRP cc_start: 0.7294 (p90) cc_final: 0.6952 (p90) REVERT: B 661 LYS cc_start: 0.8452 (ptpt) cc_final: 0.8239 (mmmm) REVERT: B 668 TYR cc_start: 0.8765 (m-80) cc_final: 0.8563 (m-80) outliers start: 21 outliers final: 15 residues processed: 187 average time/residue: 0.1797 time to fit residues: 48.7817 Evaluate side-chains 164 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 608 GLN Chi-restraints excluded: chain B residue 609 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 30.0000 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 GLN B 818 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9372 Z= 0.207 Angle : 0.576 8.696 12734 Z= 0.308 Chirality : 0.040 0.155 1426 Planarity : 0.005 0.054 1564 Dihedral : 9.720 150.575 1306 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.20 % Allowed : 14.32 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.66 (0.23), residues: 1110 helix: 0.11 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -1.53 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 397 HIS 0.008 0.001 HIS A 818 PHE 0.022 0.002 PHE B 485 TYR 0.029 0.001 TYR B 477 ARG 0.002 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.8659 (mm) cc_final: 0.8033 (tt) REVERT: A 355 LEU cc_start: 0.6032 (tp) cc_final: 0.5387 (pt) REVERT: A 650 TRP cc_start: 0.7312 (p90) cc_final: 0.7040 (p90) REVERT: B 267 TYR cc_start: 0.7205 (t80) cc_final: 0.6955 (t80) REVERT: B 348 MET cc_start: 0.7406 (ppp) cc_final: 0.7191 (ppp) REVERT: B 355 LEU cc_start: 0.6206 (tp) cc_final: 0.5603 (pt) REVERT: B 668 TYR cc_start: 0.8791 (m-80) cc_final: 0.8561 (m-80) REVERT: B 842 MET cc_start: 0.8733 (ttt) cc_final: 0.8397 (ttt) outliers start: 20 outliers final: 16 residues processed: 181 average time/residue: 0.1877 time to fit residues: 49.4567 Evaluate side-chains 161 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 566 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 818 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9372 Z= 0.168 Angle : 0.551 8.629 12734 Z= 0.290 Chirality : 0.039 0.147 1426 Planarity : 0.004 0.051 1564 Dihedral : 9.487 152.028 1306 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.09 % Allowed : 15.75 % Favored : 82.16 % 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: -0.17 (0.23), residues: 1110 helix: 0.47 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -1.28 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 397 HIS 0.004 0.001 HIS B 818 PHE 0.020 0.002 PHE A 462 TYR 0.026 0.001 TYR B 477 ARG 0.001 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 MET cc_start: 0.7566 (ptm) cc_final: 0.7070 (ppp) REVERT: A 826 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8250 (mp) REVERT: A 843 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7954 (mp0) REVERT: B 267 TYR cc_start: 0.7160 (t80) cc_final: 0.6906 (t80) REVERT: B 322 LEU cc_start: 0.8588 (mm) cc_final: 0.7937 (tt) REVERT: B 348 MET cc_start: 0.7315 (ppp) cc_final: 0.7106 (ppp) REVERT: B 530 LYS cc_start: 0.7771 (mmtt) cc_final: 0.6303 (ttpt) REVERT: B 668 TYR cc_start: 0.8742 (m-80) cc_final: 0.8514 (m-80) REVERT: B 842 MET cc_start: 0.8734 (ttt) cc_final: 0.8332 (ttt) outliers start: 19 outliers final: 16 residues processed: 175 average time/residue: 0.1724 time to fit residues: 44.3484 Evaluate side-chains 162 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.004 0.069 9372 Z= 0.248 Angle : 0.578 8.747 12734 Z= 0.305 Chirality : 0.040 0.151 1426 Planarity : 0.004 0.052 1564 Dihedral : 9.402 150.957 1306 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.97 % Allowed : 16.85 % Favored : 80.18 % 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: 0.10 (0.24), residues: 1110 helix: 0.66 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -1.15 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 397 HIS 0.008 0.001 HIS B 818 PHE 0.026 0.002 PHE A 462 TYR 0.028 0.002 TYR A 477 ARG 0.003 0.000 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8100 (tt) REVERT: A 528 TYR cc_start: 0.7957 (m-10) cc_final: 0.7541 (m-80) REVERT: A 826 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8229 (mp) REVERT: B 267 TYR cc_start: 0.7279 (t80) cc_final: 0.7044 (t80) REVERT: B 355 LEU cc_start: 0.5769 (tp) cc_final: 0.5562 (tp) REVERT: B 821 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: B 842 MET cc_start: 0.8820 (ttt) cc_final: 0.8328 (ttt) outliers start: 27 outliers final: 18 residues processed: 177 average time/residue: 0.1759 time to fit residues: 45.7427 Evaluate side-chains 164 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.0060 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 30.0000 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9372 Z= 0.177 Angle : 0.558 10.332 12734 Z= 0.290 Chirality : 0.039 0.144 1426 Planarity : 0.004 0.050 1564 Dihedral : 9.337 152.358 1306 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.30 % Allowed : 17.62 % Favored : 79.07 % 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: 0.30 (0.24), residues: 1110 helix: 0.79 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -1.03 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 397 HIS 0.008 0.001 HIS B 818 PHE 0.028 0.001 PHE A 462 TYR 0.027 0.001 TYR B 477 ARG 0.002 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8111 (tt) REVERT: A 348 MET cc_start: 0.7613 (ptm) cc_final: 0.7174 (ppp) REVERT: A 528 TYR cc_start: 0.7934 (m-10) cc_final: 0.7475 (m-80) REVERT: A 821 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: A 826 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8226 (mp) REVERT: B 267 TYR cc_start: 0.7244 (t80) cc_final: 0.7020 (t80) REVERT: B 322 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.7948 (tt) REVERT: B 528 TYR cc_start: 0.7894 (m-10) cc_final: 0.7502 (m-80) REVERT: B 821 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6957 (pm20) outliers start: 30 outliers final: 18 residues processed: 179 average time/residue: 0.1674 time to fit residues: 44.4946 Evaluate side-chains 174 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9372 Z= 0.277 Angle : 0.612 11.480 12734 Z= 0.319 Chirality : 0.041 0.145 1426 Planarity : 0.005 0.051 1564 Dihedral : 9.334 150.672 1306 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.52 % Allowed : 18.72 % Favored : 77.75 % 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: 0.39 (0.24), residues: 1110 helix: 0.87 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -1.00 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 273 HIS 0.007 0.001 HIS B 818 PHE 0.023 0.002 PHE A 462 TYR 0.027 0.002 TYR B 477 ARG 0.004 0.000 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8098 (tt) REVERT: A 348 MET cc_start: 0.7583 (ptm) cc_final: 0.6890 (ppp) REVERT: A 528 TYR cc_start: 0.7976 (m-10) cc_final: 0.7485 (m-80) REVERT: A 821 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7071 (pm20) REVERT: A 826 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 842 MET cc_start: 0.8808 (ttt) cc_final: 0.8368 (ttt) REVERT: B 267 TYR cc_start: 0.7358 (t80) cc_final: 0.7120 (t80) REVERT: B 322 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.7962 (tt) REVERT: B 821 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7125 (pm20) REVERT: B 842 MET cc_start: 0.8812 (ttt) cc_final: 0.8340 (ttt) outliers start: 32 outliers final: 22 residues processed: 175 average time/residue: 0.1776 time to fit residues: 45.4695 Evaluate side-chains 178 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9372 Z= 0.176 Angle : 0.585 13.167 12734 Z= 0.301 Chirality : 0.040 0.191 1426 Planarity : 0.004 0.049 1564 Dihedral : 9.249 152.643 1306 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.64 % Allowed : 19.82 % Favored : 77.53 % 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: 0.66 (0.24), residues: 1110 helix: 0.99 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -0.66 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 397 HIS 0.008 0.001 HIS B 818 PHE 0.022 0.001 PHE A 462 TYR 0.026 0.001 TYR B 477 ARG 0.002 0.000 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8045 (tt) REVERT: A 348 MET cc_start: 0.7502 (ptm) cc_final: 0.7037 (ppp) REVERT: A 528 TYR cc_start: 0.7920 (m-10) cc_final: 0.7530 (m-80) REVERT: A 650 TRP cc_start: 0.7368 (p90) cc_final: 0.7126 (p90) REVERT: A 821 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: A 826 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8173 (mp) REVERT: A 842 MET cc_start: 0.8722 (ttt) cc_final: 0.8344 (ttt) REVERT: B 267 TYR cc_start: 0.7310 (t80) cc_final: 0.7085 (t80) REVERT: B 322 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8065 (tt) REVERT: B 524 LEU cc_start: 0.9073 (tp) cc_final: 0.8110 (tp) REVERT: B 528 TYR cc_start: 0.7902 (m-10) cc_final: 0.7532 (m-80) REVERT: B 821 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: B 842 MET cc_start: 0.8700 (ttt) cc_final: 0.8408 (ttt) outliers start: 24 outliers final: 16 residues processed: 171 average time/residue: 0.1773 time to fit residues: 43.9895 Evaluate side-chains 174 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 0.0980 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9372 Z= 0.194 Angle : 0.585 11.612 12734 Z= 0.302 Chirality : 0.040 0.171 1426 Planarity : 0.004 0.050 1564 Dihedral : 9.170 151.867 1306 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.08 % Allowed : 19.60 % Favored : 77.31 % 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: 0.74 (0.24), residues: 1110 helix: 1.05 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -0.63 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 389 HIS 0.008 0.001 HIS B 818 PHE 0.023 0.001 PHE A 462 TYR 0.026 0.001 TYR B 477 ARG 0.002 0.000 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8201 (mmp) cc_final: 0.7927 (mmp) REVERT: A 322 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8018 (tt) REVERT: A 348 MET cc_start: 0.7496 (ptm) cc_final: 0.7007 (ppp) REVERT: A 524 LEU cc_start: 0.9041 (tp) cc_final: 0.7872 (tp) REVERT: A 528 TYR cc_start: 0.7893 (m-10) cc_final: 0.7367 (m-80) REVERT: A 650 TRP cc_start: 0.7407 (p90) cc_final: 0.7163 (p90) REVERT: A 753 ARG cc_start: 0.7081 (ptt90) cc_final: 0.6434 (ptt90) REVERT: A 821 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6961 (pm20) REVERT: A 826 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8194 (mp) REVERT: A 842 MET cc_start: 0.8726 (ttt) cc_final: 0.8341 (ttt) REVERT: B 267 TYR cc_start: 0.7318 (t80) cc_final: 0.7089 (t80) REVERT: B 322 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8036 (tt) REVERT: B 821 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: B 842 MET cc_start: 0.8744 (ttt) cc_final: 0.8521 (ttt) outliers start: 28 outliers final: 20 residues processed: 173 average time/residue: 0.1804 time to fit residues: 45.3508 Evaluate side-chains 175 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9372 Z= 0.181 Angle : 0.590 12.352 12734 Z= 0.305 Chirality : 0.040 0.171 1426 Planarity : 0.004 0.050 1564 Dihedral : 9.117 152.051 1306 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.19 % Allowed : 19.82 % Favored : 76.98 % 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: 0.87 (0.24), residues: 1110 helix: 1.15 (0.18), residues: 750 sheet: None (None), residues: 0 loop : -0.53 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.008 0.001 HIS B 818 PHE 0.024 0.001 PHE A 462 TYR 0.024 0.001 TYR B 477 ARG 0.002 0.000 ARG A 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8164 (mmp) cc_final: 0.7889 (mmp) REVERT: A 322 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8021 (tt) REVERT: A 348 MET cc_start: 0.7448 (ptm) cc_final: 0.7002 (ppp) REVERT: A 524 LEU cc_start: 0.9037 (tp) cc_final: 0.7881 (tp) REVERT: A 528 TYR cc_start: 0.7876 (m-10) cc_final: 0.7378 (m-80) REVERT: A 530 LYS cc_start: 0.8128 (mmtp) cc_final: 0.6739 (ttpt) REVERT: A 650 TRP cc_start: 0.7392 (p90) cc_final: 0.7173 (p90) REVERT: A 753 ARG cc_start: 0.7023 (ptt90) cc_final: 0.6445 (ptt90) REVERT: A 821 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: A 826 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8174 (mp) REVERT: A 842 MET cc_start: 0.8724 (ttt) cc_final: 0.8346 (ttt) REVERT: B 267 TYR cc_start: 0.7296 (t80) cc_final: 0.7069 (t80) REVERT: B 322 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8039 (tt) REVERT: B 528 TYR cc_start: 0.7865 (m-10) cc_final: 0.7548 (m-80) REVERT: B 821 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6940 (pm20) outliers start: 29 outliers final: 20 residues processed: 172 average time/residue: 0.1818 time to fit residues: 45.6024 Evaluate side-chains 179 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 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 = 0.3959 r_free = 0.3959 target = 0.139241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118040 restraints weight = 18740.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.120283 restraints weight = 12216.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.121522 restraints weight = 9093.720| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9372 Z= 0.233 Angle : 0.614 11.729 12734 Z= 0.317 Chirality : 0.041 0.154 1426 Planarity : 0.004 0.051 1564 Dihedral : 9.113 150.533 1306 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.19 % Allowed : 20.04 % Favored : 76.76 % 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: 0.75 (0.24), residues: 1110 helix: 1.05 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -0.61 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 273 HIS 0.009 0.001 HIS B 818 PHE 0.024 0.002 PHE A 462 TYR 0.034 0.002 TYR A 477 ARG 0.003 0.000 ARG A 808 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.15 seconds wall clock time: 34 minutes 33.17 seconds (2073.17 seconds total)