Starting phenix.real_space_refine on Sat Aug 23 03:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k10_36782/08_2025/8k10_36782_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k10_36782/08_2025/8k10_36782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k10_36782/08_2025/8k10_36782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k10_36782/08_2025/8k10_36782.map" model { file = "/net/cci-nas-00/data/ceres_data/8k10_36782/08_2025/8k10_36782_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k10_36782/08_2025/8k10_36782_neut.cif" } resolution = 3.2 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= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 6176 2.51 5 N 1510 2.21 5 O 1728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9478 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4627 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 568} Chain breaks: 5 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4627 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 568} Chain breaks: 5 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.18, per 1000 atoms: 0.23 Number of scatterers: 9478 At special positions: 0 Unit cell: (100.86, 74.62, 128.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1728 8.00 N 1510 7.00 C 6176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 207 " distance=2.04 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 570 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 207 " distance=2.04 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 787 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 901 " - " ASN A 27 " " NAG A 902 " - " ASN A 60 " " NAG A 903 " - " ASN A 123 " " NAG A 904 " - " ASN A 141 " " NAG B 901 " - " ASN B 27 " " NAG B 902 " - " ASN B 60 " " NAG B 903 " - " ASN B 123 " " NAG B 904 " - " ASN B 141 " " NAG C 1 " - " ASN A 165 " " NAG D 1 " - " ASN B 54 " " NAG E 1 " - " ASN B 165 " " NAG O 1 " - " ASN A 54 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 240.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 45.7% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 289 through 317 removed outlier: 4.102A pdb=" N TYR A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 479 Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.609A pdb=" N ILE A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.705A pdb=" N ILE A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 569 removed outlier: 3.623A pdb=" N LEU A 562 " --> pdb=" O MET A 558 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 596 removed outlier: 3.911A pdb=" N THR A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N MET A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 626 removed outlier: 4.369A pdb=" N PHE A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 652 removed outlier: 3.916A pdb=" N SER A 638 " --> pdb=" O TRP A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.889A pdb=" N MET A 709 " --> pdb=" O TYR A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 740 removed outlier: 3.524A pdb=" N LEU A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 767 removed outlier: 3.509A pdb=" N PHE A 761 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 794 through 816 Processing helix chain 'B' and resid 289 through 317 removed outlier: 4.171A pdb=" N TYR B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 479 Processing helix chain 'B' and resid 499 through 505 removed outlier: 3.609A pdb=" N ILE B 503 " --> pdb=" O ALA B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.705A pdb=" N ILE B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 569 removed outlier: 3.622A pdb=" N LEU B 562 " --> pdb=" O MET B 558 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 596 removed outlier: 4.131A pdb=" N THR B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N MET B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 626 removed outlier: 4.369A pdb=" N PHE B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 652 removed outlier: 3.916A pdb=" N SER B 638 " --> pdb=" O TRP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.889A pdb=" N MET B 709 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 740 removed outlier: 3.524A pdb=" N LEU B 719 " --> pdb=" O ALA B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 767 removed outlier: 3.509A pdb=" N PHE B 761 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 794 through 816 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.815A pdb=" N VAL A 57 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 126 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 43 removed outlier: 3.952A pdb=" N GLY A 64 " --> pdb=" O MET A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.160A pdb=" N LYS A 106 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 166 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 176 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.814A pdb=" N VAL B 57 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 126 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 43 removed outlier: 3.952A pdb=" N GLY B 64 " --> pdb=" O MET B 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.160A pdb=" N LYS B 106 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 155 through 156 Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 166 563 hydrogen bonds defined for protein. 1635 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: 1.56 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2857 1.34 - 1.46: 2219 1.46 - 1.58: 4510 1.58 - 1.71: 0 1.71 - 1.83: 96 Bond restraints: 9682 Sorted by residual: bond pdb=" N VAL B 182 " pdb=" CA VAL B 182 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.24e-02 6.50e+03 8.72e+00 bond pdb=" N VAL A 182 " pdb=" CA VAL A 182 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.53e+00 bond pdb=" N VAL A 288 " pdb=" CA VAL A 288 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.19e-02 7.06e+03 7.15e+00 bond pdb=" N THR A 289 " pdb=" CA THR A 289 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.14e-02 7.69e+03 6.64e+00 bond pdb=" N THR B 289 " pdb=" CA THR B 289 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.14e-02 7.69e+03 6.60e+00 ... (remaining 9677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 12651 1.70 - 3.39: 455 3.39 - 5.09: 48 5.09 - 6.79: 10 6.79 - 8.49: 4 Bond angle restraints: 13168 Sorted by residual: angle pdb=" C SER A 295 " pdb=" N GLY A 296 " pdb=" CA GLY A 296 " ideal model delta sigma weight residual 119.98 124.39 -4.41 1.11e+00 8.12e-01 1.58e+01 angle pdb=" C SER B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta sigma weight residual 119.98 124.37 -4.39 1.11e+00 8.12e-01 1.56e+01 angle pdb=" C LEU A 301 " pdb=" N GLY A 302 " pdb=" CA GLY A 302 " ideal model delta sigma weight residual 119.98 124.35 -4.37 1.11e+00 8.12e-01 1.55e+01 angle pdb=" C LEU B 301 " pdb=" N GLY B 302 " pdb=" CA GLY B 302 " ideal model delta sigma weight residual 119.98 124.22 -4.24 1.11e+00 8.12e-01 1.46e+01 angle pdb=" CA GLN B 577 " pdb=" C GLN B 577 " pdb=" O GLN B 577 " ideal model delta sigma weight residual 120.90 117.47 3.43 1.07e+00 8.73e-01 1.03e+01 ... (remaining 13163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 5051 16.19 - 32.38: 638 32.38 - 48.57: 171 48.57 - 64.77: 46 64.77 - 80.96: 10 Dihedral angle restraints: 5916 sinusoidal: 2460 harmonic: 3456 Sorted by residual: dihedral pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual 93.00 123.67 -30.67 1 1.00e+01 1.00e-02 1.34e+01 dihedral pdb=" CB CYS B 117 " pdb=" SG CYS B 117 " pdb=" SG CYS B 207 " pdb=" CB CYS B 207 " ideal model delta sinusoidal sigma weight residual 93.00 123.67 -30.67 1 1.00e+01 1.00e-02 1.34e+01 dihedral pdb=" CA LEU A 691 " pdb=" CB LEU A 691 " pdb=" CG LEU A 691 " pdb=" CD1 LEU A 691 " ideal model delta sinusoidal sigma weight residual 180.00 120.40 59.60 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1144 0.046 - 0.091: 322 0.091 - 0.137: 99 0.137 - 0.183: 33 0.183 - 0.228: 8 Chirality restraints: 1606 Sorted by residual: chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB THR A 311 " pdb=" CA THR A 311 " pdb=" OG1 THR A 311 " pdb=" CG2 THR A 311 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR B 311 " pdb=" CA THR B 311 " pdb=" OG1 THR B 311 " pdb=" CG2 THR B 311 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1603 not shown) Planarity restraints: 1636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 308 " 0.070 2.00e-02 2.50e+03 4.39e-02 3.85e+01 pdb=" CG TYR A 308 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR A 308 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 308 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 308 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR A 308 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 308 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 308 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 308 " -0.070 2.00e-02 2.50e+03 4.39e-02 3.85e+01 pdb=" CG TYR B 308 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 308 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 308 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR B 308 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR B 308 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 308 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 308 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 304 " -0.040 2.00e-02 2.50e+03 2.56e-02 1.15e+01 pdb=" CG PHE B 304 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 304 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 304 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE B 304 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 304 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 304 " -0.032 2.00e-02 2.50e+03 ... (remaining 1633 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1024 2.75 - 3.29: 9372 3.29 - 3.82: 15464 3.82 - 4.36: 17587 4.36 - 4.90: 30611 Nonbonded interactions: 74058 Sorted by model distance: nonbonded pdb=" O ALA B 194 " pdb=" OG1 THR B 226 " model vdw 2.210 3.040 nonbonded pdb=" O ALA A 194 " pdb=" OG1 THR A 226 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS A 26 " pdb=" NH2 ARG B 85 " model vdw 2.218 3.200 nonbonded pdb=" OD1 ASN A 165 " pdb=" OG1 THR A 279 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASN B 165 " pdb=" OG1 THR B 279 " model vdw 2.243 3.040 ... (remaining 74053 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'O' } 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.780 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 0.005 0.064 9706 Z= 0.282 Angle : 0.733 8.552 13232 Z= 0.432 Chirality : 0.050 0.228 1606 Planarity : 0.004 0.044 1624 Dihedral : 15.767 80.958 3648 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.39 % Allowed : 23.14 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 aren not related in a simple way. whole: 0.96 (0.24), residues: 1152 helix: 1.76 (0.22), residues: 516 sheet: 1.64 (0.28), residues: 272 loop : -1.93 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 114 TYR 0.078 0.003 TYR B 308 PHE 0.040 0.003 PHE B 304 TRP 0.009 0.002 TRP A 773 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 9682) covalent geometry : angle 0.71602 (13168) SS BOND : bond 0.00381 ( 8) SS BOND : angle 1.53476 ( 16) hydrogen bonds : bond 0.11408 ( 563) hydrogen bonds : angle 5.25002 ( 1635) link_BETA1-4 : bond 0.00300 ( 4) link_BETA1-4 : angle 0.94404 ( 12) link_NAG-ASN : bond 0.00526 ( 12) link_NAG-ASN : angle 2.92283 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7034 (tpp80) cc_final: 0.6649 (mtm-85) REVERT: A 297 MET cc_start: 0.7435 (mtt) cc_final: 0.7113 (tpp) REVERT: B 61 ARG cc_start: 0.6910 (tpp80) cc_final: 0.6580 (mtm-85) REVERT: B 297 MET cc_start: 0.7533 (mtt) cc_final: 0.7165 (tpp) outliers start: 4 outliers final: 0 residues processed: 131 average time/residue: 0.0745 time to fit residues: 14.4514 Evaluate side-chains 111 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 HIS B 796 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.219165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.168865 restraints weight = 11094.411| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.56 r_work: 0.3678 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9706 Z= 0.134 Angle : 0.535 7.294 13232 Z= 0.274 Chirality : 0.041 0.162 1606 Planarity : 0.003 0.027 1624 Dihedral : 5.837 51.098 1590 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.76 % Allowed : 24.12 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 aren not related in a simple way. whole: 1.40 (0.24), residues: 1152 helix: 2.32 (0.21), residues: 516 sheet: 1.46 (0.29), residues: 280 loop : -1.76 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 85 TYR 0.013 0.001 TYR B 173 PHE 0.015 0.002 PHE A 304 TRP 0.017 0.001 TRP B 773 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9682) covalent geometry : angle 0.51669 (13168) SS BOND : bond 0.00300 ( 8) SS BOND : angle 0.98863 ( 16) hydrogen bonds : bond 0.04194 ( 563) hydrogen bonds : angle 4.34724 ( 1635) link_BETA1-4 : bond 0.00494 ( 4) link_BETA1-4 : angle 0.94446 ( 12) link_NAG-ASN : bond 0.00481 ( 12) link_NAG-ASN : angle 2.59127 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.372 Fit side-chains REVERT: A 297 MET cc_start: 0.7643 (mtt) cc_final: 0.7124 (tpp) REVERT: B 297 MET cc_start: 0.7688 (mtt) cc_final: 0.7185 (tpp) REVERT: B 817 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7386 (tp) outliers start: 18 outliers final: 6 residues processed: 155 average time/residue: 0.0817 time to fit residues: 19.0718 Evaluate side-chains 129 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 chunk 9 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.218349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.169237 restraints weight = 11142.334| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.69 r_work: 0.3658 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9706 Z= 0.136 Angle : 0.507 6.840 13232 Z= 0.262 Chirality : 0.041 0.152 1606 Planarity : 0.003 0.026 1624 Dihedral : 5.412 42.721 1590 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.55 % Allowed : 24.31 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 aren not related in a simple way. whole: 1.52 (0.24), residues: 1152 helix: 2.50 (0.21), residues: 514 sheet: 1.41 (0.29), residues: 280 loop : -1.70 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 85 TYR 0.013 0.001 TYR B 173 PHE 0.014 0.001 PHE B 304 TRP 0.012 0.001 TRP B 773 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9682) covalent geometry : angle 0.49047 (13168) SS BOND : bond 0.00274 ( 8) SS BOND : angle 0.94058 ( 16) hydrogen bonds : bond 0.03868 ( 563) hydrogen bonds : angle 4.21490 ( 1635) link_BETA1-4 : bond 0.00326 ( 4) link_BETA1-4 : angle 0.96661 ( 12) link_NAG-ASN : bond 0.00456 ( 12) link_NAG-ASN : angle 2.40094 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.324 Fit side-chains REVERT: A 100 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8369 (ttm-80) REVERT: A 175 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8525 (tttp) REVERT: A 297 MET cc_start: 0.7615 (mtt) cc_final: 0.7095 (tpp) REVERT: B 61 ARG cc_start: 0.7002 (tpp-160) cc_final: 0.6367 (mtm-85) REVERT: B 100 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8194 (ttm-80) REVERT: B 297 MET cc_start: 0.7686 (mtt) cc_final: 0.7196 (tpp) REVERT: B 576 PHE cc_start: 0.7351 (p90) cc_final: 0.7088 (p90) REVERT: B 586 ILE cc_start: 0.8324 (tt) cc_final: 0.8122 (tp) REVERT: B 817 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7441 (tp) outliers start: 26 outliers final: 11 residues processed: 153 average time/residue: 0.0831 time to fit residues: 18.9101 Evaluate side-chains 138 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 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 = 0.4514 r_free = 0.4514 target = 0.219509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.171646 restraints weight = 11303.161| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 3.82 r_work: 0.3688 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9706 Z= 0.130 Angle : 0.503 8.977 13232 Z= 0.258 Chirality : 0.042 0.205 1606 Planarity : 0.003 0.026 1624 Dihedral : 5.036 35.947 1590 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.43 % Allowed : 23.63 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 aren not related in a simple way. whole: 1.60 (0.24), residues: 1152 helix: 2.62 (0.21), residues: 514 sheet: 1.40 (0.29), residues: 278 loop : -1.69 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 85 TYR 0.012 0.001 TYR B 173 PHE 0.012 0.001 PHE B 801 TRP 0.014 0.001 TRP B 773 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9682) covalent geometry : angle 0.48827 (13168) SS BOND : bond 0.00557 ( 8) SS BOND : angle 0.94232 ( 16) hydrogen bonds : bond 0.03666 ( 563) hydrogen bonds : angle 4.10674 ( 1635) link_BETA1-4 : bond 0.00259 ( 4) link_BETA1-4 : angle 0.95585 ( 12) link_NAG-ASN : bond 0.00432 ( 12) link_NAG-ASN : angle 2.28496 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.230 Fit side-chains REVERT: A 100 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8354 (ttm-80) REVERT: A 297 MET cc_start: 0.7669 (mtt) cc_final: 0.7208 (tpp) REVERT: B 61 ARG cc_start: 0.7092 (tpp-160) cc_final: 0.6475 (mtm-85) REVERT: B 100 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8136 (ttm-80) REVERT: B 297 MET cc_start: 0.7697 (mtt) cc_final: 0.7248 (tpp) REVERT: B 586 ILE cc_start: 0.8515 (tt) cc_final: 0.8262 (tp) REVERT: B 817 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7453 (tp) outliers start: 35 outliers final: 15 residues processed: 154 average time/residue: 0.0756 time to fit residues: 17.6331 Evaluate side-chains 141 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.215553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.162940 restraints weight = 11375.785| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 4.87 r_work: 0.3649 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9706 Z= 0.238 Angle : 0.608 14.750 13232 Z= 0.310 Chirality : 0.045 0.181 1606 Planarity : 0.003 0.035 1624 Dihedral : 5.099 35.377 1590 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.41 % Allowed : 23.43 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 aren not related in a simple way. whole: 1.48 (0.24), residues: 1152 helix: 2.49 (0.21), residues: 514 sheet: 1.16 (0.29), residues: 286 loop : -1.60 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 85 TYR 0.017 0.002 TYR A 173 PHE 0.023 0.002 PHE B 516 TRP 0.014 0.002 TRP B 773 HIS 0.006 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00576 ( 9682) covalent geometry : angle 0.59429 (13168) SS BOND : bond 0.00436 ( 8) SS BOND : angle 1.19464 ( 16) hydrogen bonds : bond 0.04102 ( 563) hydrogen bonds : angle 4.38020 ( 1635) link_BETA1-4 : bond 0.00142 ( 4) link_BETA1-4 : angle 1.14108 ( 12) link_NAG-ASN : bond 0.00401 ( 12) link_NAG-ASN : angle 2.40202 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8387 (ttm-80) REVERT: A 214 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.7253 (p0) REVERT: A 297 MET cc_start: 0.7891 (mtt) cc_final: 0.7222 (tpp) REVERT: A 785 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7852 (ptp-170) REVERT: B 100 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8333 (ttm-80) REVERT: B 214 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.7266 (p0) REVERT: B 297 MET cc_start: 0.7898 (mtt) cc_final: 0.7328 (tpp) REVERT: B 586 ILE cc_start: 0.8374 (tt) cc_final: 0.8071 (tp) outliers start: 45 outliers final: 29 residues processed: 164 average time/residue: 0.0728 time to fit residues: 17.9009 Evaluate side-chains 153 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 0.0870 chunk 105 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.218584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.171703 restraints weight = 11287.064| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.77 r_work: 0.3692 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9706 Z= 0.118 Angle : 0.541 16.219 13232 Z= 0.267 Chirality : 0.041 0.178 1606 Planarity : 0.003 0.029 1624 Dihedral : 4.711 34.162 1590 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.04 % Allowed : 24.71 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 aren not related in a simple way. whole: 1.59 (0.24), residues: 1152 helix: 2.60 (0.21), residues: 514 sheet: 1.41 (0.29), residues: 272 loop : -1.64 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.010 0.001 TYR B 173 PHE 0.020 0.001 PHE A 801 TRP 0.009 0.001 TRP B 773 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9682) covalent geometry : angle 0.52759 (13168) SS BOND : bond 0.00201 ( 8) SS BOND : angle 1.24529 ( 16) hydrogen bonds : bond 0.03546 ( 563) hydrogen bonds : angle 4.14589 ( 1635) link_BETA1-4 : bond 0.00479 ( 4) link_BETA1-4 : angle 1.07528 ( 12) link_NAG-ASN : bond 0.00423 ( 12) link_NAG-ASN : angle 2.13895 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8340 (ttm-80) REVERT: A 297 MET cc_start: 0.7708 (mtt) cc_final: 0.7225 (tpp) REVERT: B 61 ARG cc_start: 0.7058 (tpp80) cc_final: 0.6484 (mpp-170) REVERT: B 100 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8176 (ttm-80) REVERT: B 104 GLN cc_start: 0.8800 (pt0) cc_final: 0.8430 (pt0) REVERT: B 214 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.7280 (p0) REVERT: B 297 MET cc_start: 0.7693 (mtt) cc_final: 0.7335 (tpp) REVERT: B 586 ILE cc_start: 0.8590 (tt) cc_final: 0.8293 (tp) outliers start: 31 outliers final: 21 residues processed: 150 average time/residue: 0.0805 time to fit residues: 18.3254 Evaluate side-chains 144 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 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 = 0.4577 r_free = 0.4577 target = 0.218361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.165338 restraints weight = 11103.709| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 4.29 r_work: 0.3719 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9706 Z= 0.182 Angle : 0.594 14.203 13232 Z= 0.289 Chirality : 0.043 0.177 1606 Planarity : 0.003 0.027 1624 Dihedral : 4.714 32.250 1590 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.94 % Allowed : 24.71 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 aren not related in a simple way. whole: 1.54 (0.24), residues: 1152 helix: 2.56 (0.21), residues: 514 sheet: 1.27 (0.29), residues: 278 loop : -1.60 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 85 TYR 0.014 0.001 TYR B 173 PHE 0.026 0.002 PHE B 516 TRP 0.011 0.002 TRP B 773 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9682) covalent geometry : angle 0.58204 (13168) SS BOND : bond 0.00413 ( 8) SS BOND : angle 1.25560 ( 16) hydrogen bonds : bond 0.03778 ( 563) hydrogen bonds : angle 4.24875 ( 1635) link_BETA1-4 : bond 0.00217 ( 4) link_BETA1-4 : angle 1.11829 ( 12) link_NAG-ASN : bond 0.00374 ( 12) link_NAG-ASN : angle 2.15301 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8246 (ttm-80) REVERT: A 297 MET cc_start: 0.7849 (mtt) cc_final: 0.7214 (tpp) REVERT: B 61 ARG cc_start: 0.7086 (tpp80) cc_final: 0.6433 (mtm-85) REVERT: B 100 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8237 (ttm-80) REVERT: B 297 MET cc_start: 0.7828 (mtt) cc_final: 0.7327 (tpp) outliers start: 30 outliers final: 25 residues processed: 147 average time/residue: 0.0878 time to fit residues: 19.3941 Evaluate side-chains 145 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 0.0770 chunk 37 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.216068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.164070 restraints weight = 11247.187| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 3.87 r_work: 0.3660 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9706 Z= 0.131 Angle : 0.569 16.161 13232 Z= 0.273 Chirality : 0.041 0.174 1606 Planarity : 0.003 0.029 1624 Dihedral : 4.501 30.211 1590 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.84 % Allowed : 24.80 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 aren not related in a simple way. whole: 1.60 (0.24), residues: 1152 helix: 2.61 (0.21), residues: 514 sheet: 1.39 (0.29), residues: 274 loop : -1.61 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.011 0.001 TYR A 173 PHE 0.017 0.001 PHE A 801 TRP 0.009 0.001 TRP B 773 HIS 0.003 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9682) covalent geometry : angle 0.55746 (13168) SS BOND : bond 0.00243 ( 8) SS BOND : angle 1.30042 ( 16) hydrogen bonds : bond 0.03539 ( 563) hydrogen bonds : angle 4.15034 ( 1635) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 1.06304 ( 12) link_NAG-ASN : bond 0.00378 ( 12) link_NAG-ASN : angle 2.01313 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8332 (ttm-80) REVERT: A 297 MET cc_start: 0.7681 (mtt) cc_final: 0.7102 (tpp) REVERT: B 61 ARG cc_start: 0.7026 (tpp80) cc_final: 0.6436 (mtm-85) REVERT: B 100 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8173 (ttm-80) REVERT: B 104 GLN cc_start: 0.8811 (pt0) cc_final: 0.8483 (pt0) REVERT: B 297 MET cc_start: 0.7720 (mtt) cc_final: 0.7171 (tpp) REVERT: B 586 ILE cc_start: 0.8170 (tt) cc_final: 0.7952 (tp) outliers start: 29 outliers final: 25 residues processed: 145 average time/residue: 0.0810 time to fit residues: 17.7172 Evaluate side-chains 146 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.213727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.163693 restraints weight = 11129.317| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.62 r_work: 0.3632 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9706 Z= 0.178 Angle : 0.593 15.000 13232 Z= 0.290 Chirality : 0.043 0.177 1606 Planarity : 0.003 0.027 1624 Dihedral : 4.527 28.823 1590 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.14 % Allowed : 24.71 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 aren not related in a simple way. whole: 1.54 (0.24), residues: 1152 helix: 2.53 (0.21), residues: 514 sheet: 1.30 (0.29), residues: 278 loop : -1.58 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 85 TYR 0.014 0.001 TYR A 173 PHE 0.017 0.002 PHE B 516 TRP 0.014 0.002 TRP B 634 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 9682) covalent geometry : angle 0.58148 (13168) SS BOND : bond 0.00332 ( 8) SS BOND : angle 1.44342 ( 16) hydrogen bonds : bond 0.03751 ( 563) hydrogen bonds : angle 4.24544 ( 1635) link_BETA1-4 : bond 0.00225 ( 4) link_BETA1-4 : angle 1.13678 ( 12) link_NAG-ASN : bond 0.00347 ( 12) link_NAG-ASN : angle 2.04341 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8338 (ttm-80) REVERT: A 297 MET cc_start: 0.7690 (mtt) cc_final: 0.7192 (tpp) REVERT: B 61 ARG cc_start: 0.7030 (tpp80) cc_final: 0.6466 (mtm-85) REVERT: B 100 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8291 (ttm-80) REVERT: B 297 MET cc_start: 0.7750 (mtt) cc_final: 0.7281 (tpp) REVERT: B 586 ILE cc_start: 0.8329 (tt) cc_final: 0.8054 (tp) outliers start: 32 outliers final: 27 residues processed: 148 average time/residue: 0.0829 time to fit residues: 18.5870 Evaluate side-chains 145 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 90 optimal weight: 0.3980 chunk 109 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.216575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.164599 restraints weight = 11290.122| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 3.98 r_work: 0.3665 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9706 Z= 0.124 Angle : 0.568 15.051 13232 Z= 0.275 Chirality : 0.041 0.174 1606 Planarity : 0.003 0.029 1624 Dihedral : 4.289 26.957 1590 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.84 % Allowed : 24.80 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 aren not related in a simple way. whole: 1.63 (0.24), residues: 1152 helix: 2.64 (0.21), residues: 514 sheet: 1.55 (0.29), residues: 268 loop : -1.70 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.010 0.001 TYR A 173 PHE 0.020 0.001 PHE B 801 TRP 0.008 0.001 TRP B 773 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9682) covalent geometry : angle 0.55766 (13168) SS BOND : bond 0.00231 ( 8) SS BOND : angle 1.39772 ( 16) hydrogen bonds : bond 0.03453 ( 563) hydrogen bonds : angle 4.10896 ( 1635) link_BETA1-4 : bond 0.00347 ( 4) link_BETA1-4 : angle 1.05225 ( 12) link_NAG-ASN : bond 0.00363 ( 12) link_NAG-ASN : angle 1.89097 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7175 (tpp80) cc_final: 0.6498 (tmm-80) REVERT: A 100 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8292 (ttm-80) REVERT: A 297 MET cc_start: 0.7674 (mtt) cc_final: 0.7126 (tpp) REVERT: A 577 GLN cc_start: 0.8088 (pm20) cc_final: 0.7863 (pm20) REVERT: B 61 ARG cc_start: 0.6999 (tpp80) cc_final: 0.6451 (mtm-85) REVERT: B 100 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8139 (ttm-80) REVERT: B 104 GLN cc_start: 0.8846 (pt0) cc_final: 0.8502 (pt0) REVERT: B 297 MET cc_start: 0.7719 (mtt) cc_final: 0.7187 (tpp) REVERT: B 586 ILE cc_start: 0.8178 (tt) cc_final: 0.7938 (tp) outliers start: 29 outliers final: 26 residues processed: 150 average time/residue: 0.0840 time to fit residues: 18.8573 Evaluate side-chains 151 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 751 CYS Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 114 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.211964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.162934 restraints weight = 11022.845| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.85 r_work: 0.3590 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9706 Z= 0.227 Angle : 0.629 14.970 13232 Z= 0.309 Chirality : 0.044 0.181 1606 Planarity : 0.003 0.031 1624 Dihedral : 4.481 27.760 1590 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.73 % Allowed : 23.92 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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 aren not related in a simple way. whole: 1.50 (0.24), residues: 1152 helix: 2.53 (0.21), residues: 514 sheet: 1.19 (0.29), residues: 286 loop : -1.65 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 85 TYR 0.015 0.002 TYR A 173 PHE 0.027 0.002 PHE B 516 TRP 0.011 0.002 TRP B 799 HIS 0.005 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 9682) covalent geometry : angle 0.61707 (13168) SS BOND : bond 0.00400 ( 8) SS BOND : angle 1.75856 ( 16) hydrogen bonds : bond 0.03916 ( 563) hydrogen bonds : angle 4.34455 ( 1635) link_BETA1-4 : bond 0.00156 ( 4) link_BETA1-4 : angle 1.19987 ( 12) link_NAG-ASN : bond 0.00323 ( 12) link_NAG-ASN : angle 2.04207 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2527.77 seconds wall clock time: 44 minutes 4.72 seconds (2644.72 seconds total)