Starting phenix.real_space_refine on Sun Dec 29 10:11:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rx3_24723/12_2024/7rx3_24723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx3_24723/12_2024/7rx3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rx3_24723/12_2024/7rx3_24723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx3_24723/12_2024/7rx3_24723.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx3_24723/12_2024/7rx3_24723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx3_24723/12_2024/7rx3_24723.cif" } resolution = 3.3 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= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: 6.54, per 1000 atoms: 0.65 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: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.94 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: 3.01 Time building geometry restraints manager: 3.16 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 728 or resid 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 C4 or name C5 or name O01 or name O02 or name O03 or name O04 or nam \ e O11)) or (resid 903 and (name C01 or name C02 or name C03 or name C1 or name C \ 19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or nam \ e C25 or name C26 or name C27 or name C3 or name C4 or name C5 or name C6 or nam \ e C7 or name C8 or name C9 or name O01 or name O02 or name O03 or name O04 or na \ me O11 or name O12 or name O13 or name O14 or name P )) or (resid 904 and (name \ C01 or name C02 or name C03 or name C06 or name C07 or name C08 or name C1 or na \ me C10 or name 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 C2 \ 7 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 o \ r name O01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O \ 13 or name O14 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 C17 or name C19 or name C2 or name C20 or name C21 or name C22 or na \ me 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 n \ ame O03 or name O04 or name O11)) or (resid 908 and (name C01 or name C02 or nam \ e C03 or name C1 or name C19 or name C2 or name C20 or name C21 or name C22 or n \ ame 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 o \ r 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: 0.930 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.780 Find NCS groups from input model: 0.670 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: 0.010 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: 30.720 ------------------------------------------------------------------------------- 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= 0.586 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 : 6.98 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 (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: -3.98 (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 TRP 0.022 0.002 TRP A 155 HIS 0.005 0.002 HIS A 619 PHE 0.016 0.002 PHE B 253 TYR 0.013 0.002 TYR A 24 ARG 0.003 0.001 ARG B 496 *********************** 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 : 1.170 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: 0.2500 time to fit residues: 34.6565 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 : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10360 Z= 0.178 Angle : 0.586 7.437 13954 Z= 0.297 Chirality : 0.040 0.162 1522 Planarity : 0.005 0.056 1698 Dihedral : 23.609 171.080 1768 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.97 % Allowed : 10.43 % Favored : 87.60 % 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: -1.51 (0.24), residues: 1154 helix: -0.11 (0.18), residues: 808 sheet: 0.01 (0.67), residues: 44 loop : -3.55 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 155 HIS 0.003 0.001 HIS B 130 PHE 0.013 0.001 PHE B 61 TYR 0.012 0.001 TYR A 278 ARG 0.004 0.000 ARG B 250 *********************** 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 93 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 1.212 Fit side-chains REVERT: B 84 TRP cc_start: 0.6977 (m100) cc_final: 0.5172 (t60) REVERT: B 442 PHE cc_start: 0.7613 (t80) cc_final: 0.7271 (t80) REVERT: A 84 TRP cc_start: 0.6969 (m100) cc_final: 0.5132 (t60) REVERT: A 277 MET cc_start: 0.7280 (ttp) cc_final: 0.7080 (mtp) REVERT: A 442 PHE cc_start: 0.7569 (t80) cc_final: 0.7226 (t80) outliers start: 20 outliers final: 8 residues processed: 87 average time/residue: 0.2113 time to fit residues: 27.9221 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 : 1.260 ------------------------------------------------------------------------------- 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 59 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10360 Z= 0.192 Angle : 0.558 7.176 13954 Z= 0.282 Chirality : 0.039 0.163 1522 Planarity : 0.005 0.061 1698 Dihedral : 21.455 175.553 1768 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.76 % Allowed : 12.50 % Favored : 84.74 % 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 (0.26), residues: 1154 helix: 0.82 (0.19), residues: 802 sheet: 0.06 (0.67), residues: 44 loop : -3.26 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 155 HIS 0.003 0.001 HIS A 619 PHE 0.015 0.001 PHE B 61 TYR 0.010 0.001 TYR B 589 ARG 0.002 0.000 ARG A 268 *********************** 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 94 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 1.180 Fit side-chains REVERT: B 84 TRP cc_start: 0.6692 (m100) cc_final: 0.5064 (t60) REVERT: B 442 PHE cc_start: 0.7621 (t80) cc_final: 0.7331 (t80) REVERT: A 84 TRP cc_start: 0.6764 (m100) cc_final: 0.5048 (t60) REVERT: A 442 PHE cc_start: 0.7583 (t80) cc_final: 0.7274 (t80) outliers start: 28 outliers final: 15 residues processed: 89 average time/residue: 0.2090 time to fit residues: 28.3625 Evaluate side-chains 74 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 277 MET Chi-restraints excluded: chain B residue 525 PHE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 0.0000 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1949 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= 0.165 Angle : 0.536 8.842 13954 Z= 0.271 Chirality : 0.039 0.159 1522 Planarity : 0.005 0.053 1698 Dihedral : 19.882 177.303 1768 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.85 % Allowed : 13.68 % Favored : 83.46 % 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: 0.13 (0.26), residues: 1154 helix: 1.25 (0.19), residues: 802 sheet: 0.11 (0.68), residues: 44 loop : -3.18 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 155 HIS 0.002 0.001 HIS B 619 PHE 0.013 0.001 PHE A 61 TYR 0.007 0.001 TYR B 278 ARG 0.002 0.000 ARG A 562 *********************** 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 99 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 1.184 Fit side-chains REVERT: B 19 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8167 (t) REVERT: B 84 TRP cc_start: 0.6601 (m100) cc_final: 0.4954 (t60) REVERT: B 442 PHE cc_start: 0.7633 (t80) cc_final: 0.7350 (t80) REVERT: A 84 TRP cc_start: 0.6642 (m100) cc_final: 0.5029 (t60) REVERT: A 442 PHE cc_start: 0.7612 (t80) cc_final: 0.7309 (t80) outliers start: 29 outliers final: 20 residues processed: 94 average time/residue: 0.1991 time to fit residues: 28.2980 Evaluate side-chains 82 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 277 MET 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 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 327 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 94 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 97 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 429 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10360 Z= 0.200 Angle : 0.546 7.603 13954 Z= 0.276 Chirality : 0.040 0.155 1522 Planarity : 0.005 0.060 1698 Dihedral : 19.105 170.558 1768 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.44 % Allowed : 13.68 % Favored : 82.87 % 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: 0.33 (0.26), residues: 1154 helix: 1.41 (0.19), residues: 806 sheet: 0.29 (0.68), residues: 44 loop : -3.19 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 155 HIS 0.004 0.001 HIS B 619 PHE 0.015 0.001 PHE B 61 TYR 0.010 0.001 TYR A 589 ARG 0.001 0.000 ARG A 149 *********************** 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 100 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 1.064 Fit side-chains REVERT: B 84 TRP cc_start: 0.6601 (m100) cc_final: 0.4957 (t60) REVERT: B 442 PHE cc_start: 0.7636 (t80) cc_final: 0.7367 (t80) REVERT: A 84 TRP cc_start: 0.6660 (m100) cc_final: 0.5025 (t60) REVERT: A 442 PHE cc_start: 0.7614 (t80) cc_final: 0.7331 (t80) outliers start: 35 outliers final: 21 residues processed: 95 average time/residue: 0.1963 time to fit residues: 28.0953 Evaluate side-chains 82 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 327 LEU 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 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 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 38 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2157 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= 0.192 Angle : 0.542 7.172 13954 Z= 0.272 Chirality : 0.039 0.156 1522 Planarity : 0.004 0.053 1698 Dihedral : 18.282 167.713 1768 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.05 % Allowed : 14.17 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1154 helix: 1.51 (0.19), residues: 808 sheet: 0.36 (0.69), residues: 44 loop : -3.21 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 227 HIS 0.003 0.001 HIS B 619 PHE 0.014 0.001 PHE B 61 TYR 0.008 0.001 TYR B 589 ARG 0.001 0.000 ARG B 496 *********************** 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 98 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 1.153 Fit side-chains REVERT: B 19 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8166 (t) REVERT: B 84 TRP cc_start: 0.6568 (m100) cc_final: 0.4958 (t60) REVERT: B 442 PHE cc_start: 0.7631 (t80) cc_final: 0.7362 (t80) REVERT: A 84 TRP cc_start: 0.6567 (m100) cc_final: 0.4933 (t60) REVERT: A 442 PHE cc_start: 0.7607 (t80) cc_final: 0.7330 (t80) outliers start: 31 outliers final: 22 residues processed: 95 average time/residue: 0.2172 time to fit residues: 31.4349 Evaluate side-chains 86 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 323 ILE 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 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 316 LEU Chi-restraints excluded: chain A residue 323 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10360 Z= 0.387 Angle : 0.656 8.712 13954 Z= 0.329 Chirality : 0.045 0.162 1522 Planarity : 0.005 0.054 1698 Dihedral : 18.496 160.814 1768 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.54 % Allowed : 13.48 % Favored : 82.97 % 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: 0.16 (0.26), residues: 1154 helix: 1.31 (0.19), residues: 804 sheet: 0.05 (0.68), residues: 44 loop : -3.27 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 155 HIS 0.005 0.002 HIS A 619 PHE 0.022 0.002 PHE B 61 TYR 0.013 0.002 TYR A 589 ARG 0.003 0.000 ARG A 496 *********************** 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 113 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 77 time to evaluate : 1.138 Fit side-chains REVERT: B 84 TRP cc_start: 0.6768 (m100) cc_final: 0.5074 (t60) REVERT: B 442 PHE cc_start: 0.7668 (t80) cc_final: 0.7392 (t80) REVERT: A 84 TRP cc_start: 0.6833 (m100) cc_final: 0.5112 (t60) REVERT: A 442 PHE cc_start: 0.7658 (t80) cc_final: 0.7371 (t80) REVERT: A 649 MET cc_start: 0.7881 (mmt) cc_final: 0.7662 (mmp) outliers start: 36 outliers final: 32 residues processed: 106 average time/residue: 0.1902 time to fit residues: 30.7747 Evaluate side-chains 99 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 277 MET Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 328 VAL 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 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 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 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 70 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 619 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2337 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= 0.173 Angle : 0.549 8.056 13954 Z= 0.277 Chirality : 0.039 0.166 1522 Planarity : 0.004 0.052 1698 Dihedral : 17.548 163.146 1768 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.05 % Allowed : 14.67 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1154 helix: 1.59 (0.19), residues: 808 sheet: 0.22 (0.68), residues: 44 loop : -3.20 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 227 HIS 0.003 0.001 HIS A 619 PHE 0.014 0.001 PHE B 61 TYR 0.007 0.001 TYR A 18 ARG 0.002 0.000 ARG A 562 *********************** 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 99 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 1.157 Fit side-chains REVERT: B 84 TRP cc_start: 0.6689 (m100) cc_final: 0.4979 (t60) REVERT: B 442 PHE cc_start: 0.7641 (t80) cc_final: 0.7358 (t80) REVERT: B 525 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8608 (p90) REVERT: A 84 TRP cc_start: 0.6647 (m100) cc_final: 0.5005 (t60) REVERT: A 442 PHE cc_start: 0.7635 (t80) cc_final: 0.7345 (t80) REVERT: A 525 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8608 (p90) outliers start: 31 outliers final: 26 residues processed: 97 average time/residue: 0.1862 time to fit residues: 28.1946 Evaluate side-chains 93 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 277 MET 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 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 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 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 108 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 100 optimal weight: 0.2980 chunk 69 optimal weight: 0.0370 chunk 112 optimal weight: 4.9990 overall best weight: 0.3258 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10360 Z= 0.141 Angle : 0.513 7.396 13954 Z= 0.259 Chirality : 0.038 0.159 1522 Planarity : 0.004 0.044 1698 Dihedral : 16.358 164.600 1768 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.56 % Allowed : 15.16 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1154 helix: 1.81 (0.19), residues: 808 sheet: 0.55 (0.69), residues: 44 loop : -3.10 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 227 HIS 0.003 0.001 HIS B 619 PHE 0.012 0.001 PHE B 183 TYR 0.006 0.001 TYR B 352 ARG 0.002 0.000 ARG A 562 *********************** 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 106 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 1.207 Fit side-chains REVERT: B 84 TRP cc_start: 0.6410 (m100) cc_final: 0.4994 (t60) REVERT: B 442 PHE cc_start: 0.7624 (t80) cc_final: 0.7361 (t80) REVERT: A 84 TRP cc_start: 0.6472 (m100) cc_final: 0.5026 (t60) REVERT: A 442 PHE cc_start: 0.7611 (t80) cc_final: 0.7348 (t80) outliers start: 26 outliers final: 18 residues processed: 104 average time/residue: 0.1822 time to fit residues: 29.5166 Evaluate side-chains 89 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 205 LEU Chi-restraints excluded: chain B residue 316 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.0000 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 117 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 9 optimal weight: 0.0970 chunk 72 optimal weight: 0.0770 chunk 57 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.2340 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10360 Z= 0.134 Angle : 0.504 7.297 13954 Z= 0.254 Chirality : 0.038 0.151 1522 Planarity : 0.005 0.079 1698 Dihedral : 15.877 163.955 1768 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.87 % Allowed : 16.83 % Favored : 81.30 % 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: 1.06 (0.27), residues: 1154 helix: 1.94 (0.19), residues: 808 sheet: 0.98 (0.74), residues: 44 loop : -2.98 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 155 HIS 0.003 0.001 HIS B 619 PHE 0.010 0.001 PHE A 183 TYR 0.006 0.001 TYR A 278 ARG 0.002 0.000 ARG B 237 ********************** 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 92 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.896 Fit side-chains REVERT: B 84 TRP cc_start: 0.6203 (m100) cc_final: 0.5036 (t60) REVERT: B 442 PHE cc_start: 0.7614 (t80) cc_final: 0.7372 (t80) REVERT: A 84 TRP cc_start: 0.6311 (m100) cc_final: 0.5011 (t60) REVERT: A 442 PHE cc_start: 0.7607 (t80) cc_final: 0.7369 (t80) outliers start: 19 outliers final: 16 residues processed: 91 average time/residue: 0.1937 time to fit residues: 27.0878 Evaluate side-chains 85 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 205 LEU Chi-restraints excluded: chain B residue 316 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 205 LEU Chi-restraints excluded: chain A residue 323 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 96 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.135006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114061 restraints weight = 13318.451| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.15 r_work: 0.3216 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10360 Z= 0.168 Angle : 0.528 7.707 13954 Z= 0.265 Chirality : 0.039 0.143 1522 Planarity : 0.004 0.063 1698 Dihedral : 15.649 162.049 1768 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.07 % Allowed : 16.73 % Favored : 81.20 % 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: 1.07 (0.26), residues: 1154 helix: 1.94 (0.19), residues: 806 sheet: 1.10 (0.76), residues: 44 loop : -2.95 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 155 HIS 0.003 0.001 HIS B 143 PHE 0.012 0.001 PHE B 61 TYR 0.008 0.001 TYR B 589 ARG 0.002 0.000 ARG A 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.68 seconds wall clock time: 35 minutes 51.91 seconds (2151.91 seconds total)