Starting phenix.real_space_refine on Wed Feb 4 10:55:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rx3_24723/02_2026/7rx3_24723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx3_24723/02_2026/7rx3_24723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rx3_24723/02_2026/7rx3_24723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx3_24723/02_2026/7rx3_24723.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rx3_24723/02_2026/7rx3_24723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx3_24723/02_2026/7rx3_24723.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.007 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 38 5.16 5 C 6684 2.51 5 N 1600 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10130 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4786 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 565} Chain breaks: 6 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 4786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4786 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 565} Chain breaks: 6 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 279 Unusual residues: {'PGW': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 279 Unusual residues: {'PGW': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.42, per 1000 atoms: 0.24 Number of scatterers: 10130 At special positions: 0 Unit cell: (128.26, 96.46, 101.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 14 15.00 O 1794 8.00 N 1600 7.00 C 6684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 449.1 milliseconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 72.3% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.977A pdb=" N ALA B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 87 Processing helix chain 'B' and resid 104 through 117 removed outlier: 3.997A pdb=" N ILE B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.832A pdb=" N TRP B 155 " --> pdb=" O CYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.789A pdb=" N THR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 204 removed outlier: 3.741A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Proline residue: B 194 - end of helix removed outlier: 3.678A pdb=" N TRP B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.878A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.512A pdb=" N ARG B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 311 removed outlier: 3.575A pdb=" N PHE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 322 through 350 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 354 through 375 Processing helix chain 'B' and resid 375 through 383 removed outlier: 4.040A pdb=" N THR B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 422 through 435 removed outlier: 4.084A pdb=" N LEU B 426 " --> pdb=" O ASN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.820A pdb=" N GLY B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 501 removed outlier: 3.605A pdb=" N THR B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 524 removed outlier: 4.567A pdb=" N GLU B 514 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 543 removed outlier: 3.667A pdb=" N ASN B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 554 Processing helix chain 'B' and resid 568 through 592 removed outlier: 3.677A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 633 removed outlier: 4.078A pdb=" N LEU B 612 " --> pdb=" O TRP B 608 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 623 " --> pdb=" O HIS B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 659 removed outlier: 3.948A pdb=" N GLU B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 658 " --> pdb=" O TYR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 708 removed outlier: 4.120A pdb=" N MET B 707 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B 708 " --> pdb=" O PHE B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 708' Processing helix chain 'B' and resid 712 through 727 Processing helix chain 'A' and resid 28 through 46 removed outlier: 3.977A pdb=" N ALA A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 87 Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.997A pdb=" N ILE A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.833A pdb=" N TRP A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 172 removed outlier: 3.789A pdb=" N THR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 204 removed outlier: 3.741A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix removed outlier: 3.678A pdb=" N TRP A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.879A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.512A pdb=" N ARG A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 311 removed outlier: 3.575A pdb=" N PHE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 322 through 350 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 375 through 383 removed outlier: 4.041A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 422 through 435 removed outlier: 4.084A pdb=" N LEU A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.821A pdb=" N GLY A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 501 removed outlier: 3.605A pdb=" N THR A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 524 removed outlier: 4.567A pdb=" N GLU A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 543 removed outlier: 3.668A pdb=" N ASN A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'A' and resid 568 through 592 removed outlier: 3.676A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 633 removed outlier: 4.078A pdb=" N LEU A 612 " --> pdb=" O TRP A 608 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 623 " --> pdb=" O HIS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 659 removed outlier: 3.948A pdb=" N GLU A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 658 " --> pdb=" O TYR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 removed outlier: 4.120A pdb=" N MET A 707 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 708 " --> pdb=" O PHE A 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 704 through 708' Processing helix chain 'A' and resid 712 through 727 Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 54 removed outlier: 3.756A pdb=" N ARG B 53 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 61 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 22 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 19 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE B 139 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG B 21 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 256 through 257 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 54 removed outlier: 3.756A pdb=" N ARG A 53 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 61 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 22 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 19 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 139 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG A 21 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 256 through 257 590 hydrogen bonds defined for protein. 1752 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: 1.51 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1512 1.30 - 1.43: 2940 1.43 - 1.56: 5818 1.56 - 1.69: 34 1.69 - 1.82: 56 Bond restraints: 10360 Sorted by residual: bond pdb=" C1 PGW B 807 " pdb=" O01 PGW B 807 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C1 PGW A 902 " pdb=" O01 PGW A 902 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C1 PGW B 803 " pdb=" O01 PGW B 803 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C1 PGW A 906 " pdb=" O01 PGW A 906 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C1 PGW A 901 " pdb=" O01 PGW A 901 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 10355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 13028 2.35 - 4.70: 662 4.70 - 7.05: 178 7.05 - 9.40: 52 9.40 - 11.75: 34 Bond angle restraints: 13954 Sorted by residual: angle pdb=" C LYS B 158 " pdb=" N THR B 159 " pdb=" CA THR B 159 " ideal model delta sigma weight residual 121.54 132.59 -11.05 1.91e+00 2.74e-01 3.34e+01 angle pdb=" C LYS A 158 " pdb=" N THR A 159 " pdb=" CA THR A 159 " ideal model delta sigma weight residual 121.54 132.57 -11.03 1.91e+00 2.74e-01 3.33e+01 angle pdb=" N VAL A 508 " pdb=" CA VAL A 508 " pdb=" C VAL A 508 " ideal model delta sigma weight residual 112.96 107.84 5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" N VAL B 508 " pdb=" CA VAL B 508 " pdb=" C VAL B 508 " ideal model delta sigma weight residual 112.96 107.87 5.09 1.00e+00 1.00e+00 2.59e+01 angle pdb=" C LEU A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 120.24 123.42 -3.18 6.30e-01 2.52e+00 2.54e+01 ... (remaining 13949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.51: 5819 32.51 - 65.03: 321 65.03 - 97.54: 62 97.54 - 130.05: 16 130.05 - 162.56: 14 Dihedral angle restraints: 6232 sinusoidal: 2754 harmonic: 3478 Sorted by residual: dihedral pdb=" CA VAL B 117 " pdb=" C VAL B 117 " pdb=" N PRO B 118 " pdb=" CA PRO B 118 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL A 117 " pdb=" C VAL A 117 " pdb=" N PRO A 118 " pdb=" CA PRO A 118 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" O01 PGW A 905 " pdb=" C01 PGW A 905 " pdb=" C02 PGW A 905 " pdb=" O03 PGW A 905 " ideal model delta sinusoidal sigma weight residual 59.30 -103.26 162.56 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 6229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1003 0.049 - 0.098: 376 0.098 - 0.147: 104 0.147 - 0.197: 29 0.197 - 0.246: 10 Chirality restraints: 1522 Sorted by residual: chirality pdb=" C02 PGW B 806 " pdb=" C01 PGW B 806 " pdb=" C03 PGW B 806 " pdb=" O01 PGW B 806 " both_signs ideal model delta sigma weight residual False 2.36 2.60 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C02 PGW A 901 " pdb=" C01 PGW A 901 " pdb=" C03 PGW A 901 " pdb=" O01 PGW A 901 " both_signs ideal model delta sigma weight residual False 2.36 2.60 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE B 332 " pdb=" CA ILE B 332 " pdb=" CG1 ILE B 332 " pdb=" CG2 ILE B 332 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1519 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 317 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LYS A 317 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS A 317 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY A 318 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 317 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C LYS B 317 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS B 317 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY B 318 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 422 " -0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO A 423 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " -0.042 5.00e-02 4.00e+02 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3228 2.84 - 3.36: 8979 3.36 - 3.87: 16186 3.87 - 4.39: 18423 4.39 - 4.90: 32680 Nonbonded interactions: 79496 Sorted by model distance: nonbonded pdb=" O SER B 420 " pdb=" OG SER B 420 " model vdw 2.327 3.040 nonbonded pdb=" O SER A 420 " pdb=" OG SER A 420 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR A 589 " pdb=" O ILE A 605 " model vdw 2.350 3.040 nonbonded pdb=" OH TYR B 589 " pdb=" O ILE B 605 " model vdw 2.350 3.040 nonbonded pdb=" O SER A 207 " pdb=" OAE PGW A 905 " model vdw 2.359 3.040 ... (remaining 79491 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 901 or (resid 902 and (name C01 or name C02 or \ name C03 or name C15 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C \ 4 or name C5 or name O01 or name O02 or name O03 or name O04 or name O11)) or (r \ esid 903 and (name C01 or name C02 or name C03 or name C1 or name C19 or name C2 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C3 or name C4 or name C5 or name C6 or name C7 or name \ C8 or name C9 or name O01 or name O02 or name O03 or name O04 or name O11 or nam \ e O12 or name O13 or name O14 or name P )) or (resid 904 and (name C01 or name C \ 02 or name C03 or name C06 or name C07 or name C08 or name C1 or name C10 or nam \ e C15 or name C16 or name C17 or name C19 or name C2 or name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 or \ name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name O1 \ 4 or name P )) or resid 905 through 906 or (resid 907 and (name C01 or name C02 \ or name C03 or name C06 or name C1 or name C10 or name C15 or name C16 or name C \ 17 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C5 or na \ me C6 or name C7 or name C8 or name C9 or name O01 or name O02 or name O03 or na \ me O04 or name O11)) or (resid 908 and (name C01 or name C02 or name C03 or name \ C1 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or na \ me C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C5 or n \ ame C6 or name C7 or name O01 or name O02 or name O03 or name O04 or name O11 or \ name O12 or name O13 or name O14 or name P )))) selection = (chain 'B' and (resid 11 through 728 or (resid 801 and (name C01 or name C02 or \ name C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C \ 25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name \ O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name O14 or n \ ame P )) or (resid 802 and (name C01 or name C02 or name C03 or name C15 or name \ C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or n \ ame C25 or name C26 or name C27 or name C3 or name C4 or name C5 or name O01 or \ name O02 or name O03 or name O04 or name O11)) or (resid 803 and (name C01 or na \ me C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 or \ name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name O1 \ 4 or name P )) or (resid 804 and (name C01 or name C02 or name C03 or name C06 o \ r name C07 or name C08 or name C1 or name C10 or name C15 or name C16 or name C1 \ 7 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C5 or nam \ e C6 or name C7 or name C8 or name C9 or name O01 or name O02 or name O03 or nam \ e O04 or name O11 or name O12 or name O13 or name O14 or name P )) or (resid 805 \ and (name C01 or name C02 or name C03 or name C04 or name C05 or name C1 or nam \ e C15 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C5 or \ name CAD or name O01 or name O02 or name O03 or name O04 or name O11 or name O1 \ 2 or name O13 or name O14 or name OAE or name OAF or name P )) or (resid 806 and \ (name C01 or name C02 or name C03 or name C1 or name C15 or name C19 or name C2 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C3 or name C4 or name C5 or name C6 or name C7 or name \ C8 or name C9 or name O01 or name O02 or name O03 or name O04 or name O11 or nam \ e O12 or name O13 or name O14 or name P )) or resid 807 or (resid 808 and (name \ C01 or name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or nam \ e C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name O01 or name O02 or \ name O03 or name O04 or name O11 or name O12 or name O13 or name O14 or name P ) \ ))) } 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 individual isotropic 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.990 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 0.092 10360 Z= 0.440 Angle : 1.375 11.750 13954 Z= 0.635 Chirality : 0.059 0.246 1522 Planarity : 0.008 0.076 1698 Dihedral : 22.826 162.563 3972 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.20 % Allowed : 8.27 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.19), residues: 1154 helix: -2.14 (0.13), residues: 800 sheet: -1.01 (0.71), residues: 44 loop : -3.82 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 496 TYR 0.013 0.002 TYR A 24 PHE 0.016 0.002 PHE B 253 TRP 0.022 0.002 TRP A 155 HIS 0.005 0.002 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00929 (10360) covalent geometry : angle 1.37457 (13954) hydrogen bonds : bond 0.12409 ( 590) hydrogen bonds : angle 5.62740 ( 1752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.359 Fit side-chains REVERT: B 84 TRP cc_start: 0.7073 (m100) cc_final: 0.5199 (t60) REVERT: B 442 PHE cc_start: 0.7746 (t80) cc_final: 0.7439 (t80) REVERT: A 84 TRP cc_start: 0.6945 (m100) cc_final: 0.5172 (t60) REVERT: A 442 PHE cc_start: 0.7706 (t80) cc_final: 0.7368 (t80) outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.1073 time to fit residues: 15.0766 Evaluate side-chains 58 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 280 GLN B 283 GLN B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN A 280 GLN A 283 GLN A 364 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114453 restraints weight = 13638.921| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.35 r_work: 0.3236 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10360 Z= 0.132 Angle : 0.593 7.493 13954 Z= 0.301 Chirality : 0.040 0.160 1522 Planarity : 0.005 0.055 1698 Dihedral : 23.667 172.405 1768 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.97 % Allowed : 10.63 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.24), residues: 1154 helix: -0.12 (0.18), residues: 806 sheet: -0.05 (0.67), residues: 44 loop : -3.49 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 250 TYR 0.012 0.001 TYR A 278 PHE 0.015 0.001 PHE B 61 TRP 0.010 0.001 TRP A 227 HIS 0.003 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00310 (10360) covalent geometry : angle 0.59315 (13954) hydrogen bonds : bond 0.03740 ( 590) hydrogen bonds : angle 4.14290 ( 1752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.442 Fit side-chains REVERT: B 84 TRP cc_start: 0.7103 (m100) cc_final: 0.4869 (t60) REVERT: B 277 MET cc_start: 0.8072 (ttp) cc_final: 0.7647 (mtp) REVERT: B 442 PHE cc_start: 0.7615 (t80) cc_final: 0.7267 (t80) REVERT: A 84 TRP cc_start: 0.7132 (m100) cc_final: 0.4856 (t60) REVERT: A 442 PHE cc_start: 0.7570 (t80) cc_final: 0.7227 (t80) outliers start: 20 outliers final: 8 residues processed: 88 average time/residue: 0.0905 time to fit residues: 12.0696 Evaluate side-chains 69 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 0.0170 chunk 63 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109243 restraints weight = 13857.855| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.38 r_work: 0.3138 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10360 Z= 0.247 Angle : 0.673 8.320 13954 Z= 0.340 Chirality : 0.044 0.166 1522 Planarity : 0.005 0.062 1698 Dihedral : 22.391 179.198 1768 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.25 % Allowed : 12.70 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.25), residues: 1154 helix: 0.52 (0.19), residues: 796 sheet: -0.05 (0.67), residues: 44 loop : -3.27 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 149 TYR 0.014 0.002 TYR B 589 PHE 0.022 0.002 PHE B 61 TRP 0.018 0.002 TRP B 155 HIS 0.005 0.002 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00616 (10360) covalent geometry : angle 0.67336 (13954) hydrogen bonds : bond 0.04475 ( 590) hydrogen bonds : angle 4.17411 ( 1752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.388 Fit side-chains REVERT: B 84 TRP cc_start: 0.7172 (m100) cc_final: 0.4912 (t60) REVERT: B 442 PHE cc_start: 0.7623 (t80) cc_final: 0.7294 (t80) REVERT: A 84 TRP cc_start: 0.7149 (m100) cc_final: 0.4890 (t60) REVERT: A 442 PHE cc_start: 0.7598 (t80) cc_final: 0.7261 (t80) outliers start: 33 outliers final: 22 residues processed: 95 average time/residue: 0.0795 time to fit residues: 11.8830 Evaluate side-chains 84 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 712 TRP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 712 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 0.9980 chunk 104 optimal weight: 0.0770 chunk 40 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 68 optimal weight: 0.0050 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.5752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** 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 = 0.3633 r_free = 0.3633 target = 0.133245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110706 restraints weight = 13347.998| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.42 r_work: 0.3176 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10360 Z= 0.111 Angle : 0.546 9.121 13954 Z= 0.278 Chirality : 0.039 0.160 1522 Planarity : 0.005 0.054 1698 Dihedral : 20.561 175.136 1768 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.26 % Allowed : 14.67 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.26), residues: 1154 helix: 1.04 (0.19), residues: 802 sheet: 0.01 (0.66), residues: 44 loop : -3.21 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 562 TYR 0.008 0.001 TYR B 278 PHE 0.013 0.001 PHE B 61 TRP 0.019 0.001 TRP B 155 HIS 0.002 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00252 (10360) covalent geometry : angle 0.54646 (13954) hydrogen bonds : bond 0.03167 ( 590) hydrogen bonds : angle 3.69517 ( 1752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.372 Fit side-chains REVERT: B 19 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8521 (t) REVERT: B 84 TRP cc_start: 0.6684 (m100) cc_final: 0.4604 (t60) REVERT: B 442 PHE cc_start: 0.7486 (t80) cc_final: 0.7127 (t80) REVERT: A 84 TRP cc_start: 0.6768 (m100) cc_final: 0.4628 (t60) REVERT: A 442 PHE cc_start: 0.7472 (t80) cc_final: 0.7122 (t80) outliers start: 23 outliers final: 16 residues processed: 89 average time/residue: 0.0887 time to fit residues: 11.9493 Evaluate side-chains 79 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** 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 = 0.3628 r_free = 0.3628 target = 0.132821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110575 restraints weight = 13356.722| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.22 r_work: 0.3167 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10360 Z= 0.119 Angle : 0.543 8.181 13954 Z= 0.274 Chirality : 0.039 0.153 1522 Planarity : 0.005 0.057 1698 Dihedral : 19.346 171.005 1768 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.54 % Allowed : 13.98 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1154 helix: 1.29 (0.19), residues: 808 sheet: 0.14 (0.67), residues: 44 loop : -3.27 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 562 TYR 0.008 0.001 TYR B 589 PHE 0.014 0.001 PHE B 61 TRP 0.010 0.001 TRP B 227 HIS 0.003 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00284 (10360) covalent geometry : angle 0.54279 (13954) hydrogen bonds : bond 0.03220 ( 590) hydrogen bonds : angle 3.65433 ( 1752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.485 Fit side-chains REVERT: B 19 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8486 (t) REVERT: B 84 TRP cc_start: 0.6626 (m100) cc_final: 0.4651 (t60) REVERT: B 442 PHE cc_start: 0.7598 (t80) cc_final: 0.7274 (t80) REVERT: A 84 TRP cc_start: 0.6691 (m100) cc_final: 0.4683 (t60) REVERT: A 442 PHE cc_start: 0.7566 (t80) cc_final: 0.7233 (t80) outliers start: 36 outliers final: 20 residues processed: 95 average time/residue: 0.0878 time to fit residues: 12.7198 Evaluate side-chains 80 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107303 restraints weight = 13442.662| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.21 r_work: 0.3113 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10360 Z= 0.182 Angle : 0.601 8.323 13954 Z= 0.302 Chirality : 0.042 0.156 1522 Planarity : 0.005 0.056 1698 Dihedral : 19.029 164.997 1768 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.44 % Allowed : 14.96 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.26), residues: 1154 helix: 1.29 (0.19), residues: 804 sheet: -0.01 (0.68), residues: 44 loop : -3.25 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 496 TYR 0.012 0.001 TYR A 589 PHE 0.019 0.002 PHE A 61 TRP 0.010 0.001 TRP A 227 HIS 0.005 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00453 (10360) covalent geometry : angle 0.60090 (13954) hydrogen bonds : bond 0.03865 ( 590) hydrogen bonds : angle 3.80561 ( 1752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.399 Fit side-chains REVERT: B 84 TRP cc_start: 0.6870 (m100) cc_final: 0.4804 (t60) REVERT: B 137 ASP cc_start: 0.8192 (t0) cc_final: 0.7937 (t0) REVERT: B 442 PHE cc_start: 0.7607 (t80) cc_final: 0.7273 (t80) REVERT: A 84 TRP cc_start: 0.6835 (m100) cc_final: 0.4716 (t60) REVERT: A 442 PHE cc_start: 0.7593 (t80) cc_final: 0.7264 (t80) outliers start: 35 outliers final: 27 residues processed: 106 average time/residue: 0.0841 time to fit residues: 13.6656 Evaluate side-chains 93 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 712 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.128373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106253 restraints weight = 13391.056| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.35 r_work: 0.3096 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10360 Z= 0.203 Angle : 0.616 8.024 13954 Z= 0.311 Chirality : 0.043 0.159 1522 Planarity : 0.005 0.056 1698 Dihedral : 18.691 159.195 1768 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.94 % Allowed : 15.26 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.26), residues: 1154 helix: 1.23 (0.19), residues: 806 sheet: -0.08 (0.68), residues: 44 loop : -3.20 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 496 TYR 0.012 0.001 TYR A 589 PHE 0.019 0.002 PHE B 61 TRP 0.009 0.001 TRP A 227 HIS 0.005 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00509 (10360) covalent geometry : angle 0.61593 (13954) hydrogen bonds : bond 0.03934 ( 590) hydrogen bonds : angle 3.86505 ( 1752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 74 time to evaluate : 0.379 Fit side-chains REVERT: B 84 TRP cc_start: 0.6889 (m100) cc_final: 0.4771 (t60) REVERT: B 442 PHE cc_start: 0.7617 (t80) cc_final: 0.7298 (t80) REVERT: A 84 TRP cc_start: 0.6892 (m100) cc_final: 0.4784 (t60) REVERT: A 442 PHE cc_start: 0.7570 (t80) cc_final: 0.7238 (t80) outliers start: 40 outliers final: 33 residues processed: 108 average time/residue: 0.0777 time to fit residues: 13.1325 Evaluate side-chains 103 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 712 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 HIS ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.132479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108342 restraints weight = 13309.432| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.35 r_work: 0.3136 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10360 Z= 0.113 Angle : 0.538 7.431 13954 Z= 0.270 Chirality : 0.039 0.153 1522 Planarity : 0.004 0.056 1698 Dihedral : 17.686 161.903 1768 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.15 % Allowed : 16.04 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.26), residues: 1154 helix: 1.49 (0.19), residues: 808 sheet: 0.14 (0.68), residues: 44 loop : -3.14 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.007 0.001 TYR A 18 PHE 0.014 0.001 PHE B 61 TRP 0.012 0.001 TRP A 227 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00265 (10360) covalent geometry : angle 0.53768 (13954) hydrogen bonds : bond 0.03092 ( 590) hydrogen bonds : angle 3.65109 ( 1752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.374 Fit side-chains REVERT: B 19 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8481 (t) REVERT: B 84 TRP cc_start: 0.6617 (m100) cc_final: 0.4602 (t60) REVERT: B 353 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7059 (tp30) REVERT: B 442 PHE cc_start: 0.7528 (t80) cc_final: 0.7182 (t80) REVERT: A 84 TRP cc_start: 0.6651 (m100) cc_final: 0.4619 (t60) REVERT: A 442 PHE cc_start: 0.7513 (t80) cc_final: 0.7183 (t80) outliers start: 32 outliers final: 25 residues processed: 98 average time/residue: 0.0839 time to fit residues: 12.7034 Evaluate side-chains 90 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 0.0040 chunk 28 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** 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 = 0.3648 r_free = 0.3648 target = 0.134499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110656 restraints weight = 13355.731| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.34 r_work: 0.3169 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10360 Z= 0.108 Angle : 0.530 8.021 13954 Z= 0.265 Chirality : 0.038 0.148 1522 Planarity : 0.004 0.057 1698 Dihedral : 16.787 163.177 1768 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.76 % Allowed : 16.63 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.27), residues: 1154 helix: 1.68 (0.19), residues: 810 sheet: 0.30 (0.69), residues: 44 loop : -3.12 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 562 TYR 0.008 0.001 TYR A 352 PHE 0.015 0.001 PHE B 183 TRP 0.012 0.001 TRP B 227 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00255 (10360) covalent geometry : angle 0.53031 (13954) hydrogen bonds : bond 0.02892 ( 590) hydrogen bonds : angle 3.52876 ( 1752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.397 Fit side-chains REVERT: B 84 TRP cc_start: 0.6562 (m100) cc_final: 0.4638 (t60) REVERT: B 353 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7051 (tp30) REVERT: B 442 PHE cc_start: 0.7500 (t80) cc_final: 0.7183 (t80) REVERT: A 84 TRP cc_start: 0.6556 (m100) cc_final: 0.4637 (t60) REVERT: A 442 PHE cc_start: 0.7495 (t80) cc_final: 0.7176 (t80) outliers start: 28 outliers final: 24 residues processed: 100 average time/residue: 0.0825 time to fit residues: 12.9191 Evaluate side-chains 91 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.0470 chunk 82 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** 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 = 0.3627 r_free = 0.3627 target = 0.132945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109027 restraints weight = 13275.094| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.34 r_work: 0.3145 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10360 Z= 0.123 Angle : 0.536 7.224 13954 Z= 0.270 Chirality : 0.040 0.168 1522 Planarity : 0.005 0.074 1698 Dihedral : 16.559 161.995 1768 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.36 % Allowed : 17.13 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.27), residues: 1154 helix: 1.72 (0.19), residues: 810 sheet: 0.52 (0.71), residues: 44 loop : -3.17 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 237 TYR 0.008 0.001 TYR B 589 PHE 0.014 0.001 PHE B 61 TRP 0.010 0.001 TRP A 227 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00300 (10360) covalent geometry : angle 0.53629 (13954) hydrogen bonds : bond 0.03110 ( 590) hydrogen bonds : angle 3.54327 ( 1752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.319 Fit side-chains REVERT: B 84 TRP cc_start: 0.6584 (m100) cc_final: 0.4637 (t60) REVERT: B 442 PHE cc_start: 0.7522 (t80) cc_final: 0.7203 (t80) REVERT: A 84 TRP cc_start: 0.6631 (m100) cc_final: 0.4645 (t60) REVERT: A 442 PHE cc_start: 0.7516 (t80) cc_final: 0.7199 (t80) outliers start: 24 outliers final: 23 residues processed: 94 average time/residue: 0.0831 time to fit residues: 12.0965 Evaluate side-chains 92 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** 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 = 0.3645 r_free = 0.3645 target = 0.134282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110620 restraints weight = 13423.645| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.32 r_work: 0.3170 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10360 Z= 0.107 Angle : 0.526 7.328 13954 Z= 0.265 Chirality : 0.039 0.164 1522 Planarity : 0.004 0.063 1698 Dihedral : 16.143 162.126 1768 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.26 % Allowed : 17.42 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.27), residues: 1154 helix: 1.78 (0.19), residues: 812 sheet: 0.68 (0.72), residues: 44 loop : -3.13 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 237 TYR 0.007 0.001 TYR B 352 PHE 0.012 0.001 PHE B 61 TRP 0.012 0.001 TRP B 227 HIS 0.002 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00253 (10360) covalent geometry : angle 0.52552 (13954) hydrogen bonds : bond 0.02855 ( 590) hydrogen bonds : angle 3.46475 ( 1752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.93 seconds wall clock time: 41 minutes 54.89 seconds (2514.89 seconds total)