Starting phenix.real_space_refine on Fri Mar 14 02:40:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k10_36782/03_2025/8k10_36782_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k10_36782/03_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_36782/03_2025/8k10_36782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k10_36782/03_2025/8k10_36782.map" model { file = "/net/cci-nas-00/data/ceres_data/8k10_36782/03_2025/8k10_36782_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k10_36782/03_2025/8k10_36782_neut.cif" } resolution = 3.2 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= 0.057 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 2, 'TRP:plan': 1, '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: {'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 2, 'TRP:plan': 1, '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: 6.58, per 1000 atoms: 0.69 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: 2.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.93 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: 2.97 Time building geometry restraints manager: 3.39 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: 0.05 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: 0.010 Normalize map: mean=0, sd=1: 1.550 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.420 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- 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 9682 Z= 0.332 Angle : 0.716 8.487 13168 Z= 0.429 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 (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: 0.96 (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 TRP 0.009 0.002 TRP A 773 HIS 0.003 0.001 HIS A 55 PHE 0.040 0.003 PHE B 304 TYR 0.078 0.003 TYR B 308 ARG 0.001 0.000 ARG B 114 *********************** 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 : 1.101 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: 0.1939 time to fit residues: 37.6113 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 : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 90 optimal weight: 0.0870 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.0964 ------------------------------------------------------------------------------- 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 = 0.4491 r_free = 0.4491 target = 0.217682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.168697 restraints weight = 11081.774| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.70 r_work: 0.3649 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9682 Z= 0.237 Angle : 0.535 6.911 13168 Z= 0.281 Chirality : 0.042 0.167 1606 Planarity : 0.003 0.028 1624 Dihedral : 6.023 51.881 1590 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.96 % Allowed : 24.41 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.32 (0.24), residues: 1152 helix: 2.25 (0.21), residues: 520 sheet: 1.40 (0.29), residues: 280 loop : -1.81 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 773 HIS 0.004 0.001 HIS A 55 PHE 0.019 0.002 PHE A 304 TYR 0.014 0.001 TYR B 173 ARG 0.007 0.000 ARG A 85 *********************** 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 157 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.077 Fit side-chains REVERT: A 100 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8283 (ttm-80) REVERT: A 297 MET cc_start: 0.7694 (mtt) cc_final: 0.7148 (tpp) REVERT: A 736 MET cc_start: 0.7258 (mmm) cc_final: 0.6729 (mtt) REVERT: B 297 MET cc_start: 0.7706 (mtt) cc_final: 0.7178 (tpp) REVERT: B 817 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7382 (tp) outliers start: 20 outliers final: 7 residues processed: 151 average time/residue: 0.1789 time to fit residues: 40.4795 Evaluate side-chains 128 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 751 CYS 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 37 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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** A 796 HIS B 506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.215618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.169163 restraints weight = 11199.121| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.46 r_work: 0.3659 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9682 Z= 0.355 Angle : 0.573 6.731 13168 Z= 0.302 Chirality : 0.044 0.169 1606 Planarity : 0.004 0.032 1624 Dihedral : 5.720 41.366 1590 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.90 % Allowed : 22.25 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.40 (0.24), residues: 1152 helix: 2.39 (0.21), residues: 514 sheet: 1.29 (0.29), residues: 280 loop : -1.69 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 773 HIS 0.004 0.001 HIS B 55 PHE 0.016 0.002 PHE B 516 TYR 0.016 0.002 TYR B 173 ARG 0.005 0.001 ARG A 85 *********************** 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 176 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8303 (ttm-80) REVERT: A 214 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.7295 (p0) REVERT: A 297 MET cc_start: 0.7738 (mtt) cc_final: 0.7263 (tpp) REVERT: B 100 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8313 (ttm-80) REVERT: B 214 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.7389 (p0) REVERT: B 297 MET cc_start: 0.7751 (mtt) cc_final: 0.7397 (tpp) outliers start: 50 outliers final: 30 residues processed: 165 average time/residue: 0.1893 time to fit residues: 46.8239 Evaluate side-chains 145 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 303 ILE 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 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 214 ASN Chi-restraints excluded: chain B residue 232 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 11 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 B 796 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.216551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.168674 restraints weight = 11180.860| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.57 r_work: 0.3673 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9682 Z= 0.261 Angle : 0.519 6.715 13168 Z= 0.275 Chirality : 0.042 0.185 1606 Planarity : 0.003 0.030 1624 Dihedral : 5.328 37.474 1590 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.22 % Allowed : 24.02 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.49 (0.24), residues: 1152 helix: 2.54 (0.21), residues: 514 sheet: 1.27 (0.29), residues: 280 loop : -1.71 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 773 HIS 0.004 0.001 HIS A 55 PHE 0.019 0.002 PHE B 516 TYR 0.013 0.001 TYR B 173 ARG 0.004 0.000 ARG A 85 *********************** 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 168 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8359 (ttm-80) REVERT: A 297 MET cc_start: 0.7705 (mtt) cc_final: 0.7348 (tpp) REVERT: B 100 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8346 (ttm-80) REVERT: B 297 MET cc_start: 0.7766 (mtt) cc_final: 0.7371 (tpp) outliers start: 43 outliers final: 29 residues processed: 157 average time/residue: 0.1771 time to fit residues: 41.9155 Evaluate side-chains 148 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 175 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 574 THR 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 100 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 127 ILE 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 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 812 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 104 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4515 r_free = 0.4515 target = 0.219837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.170822 restraints weight = 11111.070| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.77 r_work: 0.3666 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9682 Z= 0.213 Angle : 0.522 10.731 13168 Z= 0.267 Chirality : 0.042 0.179 1606 Planarity : 0.003 0.029 1624 Dihedral : 5.058 36.365 1590 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.22 % Allowed : 24.02 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.54 (0.24), residues: 1152 helix: 2.56 (0.21), residues: 514 sheet: 1.28 (0.29), residues: 280 loop : -1.64 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 773 HIS 0.003 0.001 HIS B 55 PHE 0.019 0.002 PHE A 801 TYR 0.012 0.001 TYR B 173 ARG 0.004 0.000 ARG A 85 *********************** 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 171 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8310 (ttm-80) REVERT: A 297 MET cc_start: 0.7653 (mtt) cc_final: 0.7247 (tpp) REVERT: A 585 MET cc_start: 0.8493 (tmm) cc_final: 0.8279 (tmm) REVERT: B 61 ARG cc_start: 0.7045 (tpp80) cc_final: 0.6404 (mtm-85) REVERT: B 100 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8300 (ttm-80) REVERT: B 297 MET cc_start: 0.7731 (mtt) cc_final: 0.7377 (tpp) REVERT: B 514 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7050 (tt) REVERT: B 586 ILE cc_start: 0.8499 (tt) cc_final: 0.8225 (tp) outliers start: 43 outliers final: 30 residues processed: 161 average time/residue: 0.1718 time to fit residues: 41.3536 Evaluate side-chains 151 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 136 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 175 LYS 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 283 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 549 LEU 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 127 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 514 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4511 r_free = 0.4511 target = 0.219600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.174756 restraints weight = 11176.695| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 3.47 r_work: 0.3708 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9682 Z= 0.179 Angle : 0.540 14.601 13168 Z= 0.267 Chirality : 0.041 0.174 1606 Planarity : 0.003 0.027 1624 Dihedral : 4.796 34.712 1590 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.82 % Allowed : 24.90 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.58 (0.24), residues: 1152 helix: 2.63 (0.21), residues: 514 sheet: 1.29 (0.29), residues: 280 loop : -1.67 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 773 HIS 0.003 0.001 HIS A 55 PHE 0.020 0.001 PHE B 801 TYR 0.011 0.001 TYR B 173 ARG 0.004 0.000 ARG B 85 *********************** 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 170 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6990 (tpp80) cc_final: 0.6450 (mtm-85) REVERT: A 297 MET cc_start: 0.7554 (mtt) cc_final: 0.7239 (tpp) REVERT: A 585 MET cc_start: 0.8479 (tmm) cc_final: 0.8233 (tmm) REVERT: B 61 ARG cc_start: 0.7131 (tpp80) cc_final: 0.6599 (mpp-170) REVERT: B 100 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8177 (ttm-80) REVERT: B 104 GLN cc_start: 0.8803 (pt0) cc_final: 0.8402 (pt0) REVERT: B 297 MET cc_start: 0.7665 (mtt) cc_final: 0.7392 (tpp) REVERT: B 586 ILE cc_start: 0.8485 (tt) cc_final: 0.8197 (tp) outliers start: 39 outliers final: 30 residues processed: 164 average time/residue: 0.2019 time to fit residues: 50.3385 Evaluate side-chains 152 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 95 VAL 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 148 VAL Chi-restraints excluded: chain A residue 174 PHE 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 498 SER Chi-restraints excluded: chain A residue 549 LEU 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 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 174 PHE 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 562 LEU 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 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 82 optimal weight: 0.0020 chunk 97 optimal weight: 0.0980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS ** A 575 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 = 0.4510 r_free = 0.4510 target = 0.219461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171972 restraints weight = 11226.194| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 3.86 r_work: 0.3694 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9682 Z= 0.149 Angle : 0.554 15.025 13168 Z= 0.268 Chirality : 0.041 0.166 1606 Planarity : 0.003 0.029 1624 Dihedral : 4.609 33.099 1590 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.24 % Allowed : 25.00 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.61 (0.24), residues: 1152 helix: 2.62 (0.21), residues: 514 sheet: 1.45 (0.29), residues: 272 loop : -1.66 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 773 HIS 0.002 0.001 HIS B 55 PHE 0.024 0.001 PHE B 516 TYR 0.010 0.001 TYR B 173 ARG 0.005 0.000 ARG B 150 *********************** 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 167 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7001 (tpp80) cc_final: 0.6429 (mtm-85) REVERT: A 297 MET cc_start: 0.7591 (mtt) cc_final: 0.7221 (tpp) REVERT: A 574 THR cc_start: 0.8101 (p) cc_final: 0.7874 (p) REVERT: A 585 MET cc_start: 0.8438 (tmm) cc_final: 0.8168 (tmm) REVERT: B 61 ARG cc_start: 0.7054 (tpp80) cc_final: 0.6511 (mtm-85) REVERT: B 100 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8112 (ttm-80) REVERT: B 104 GLN cc_start: 0.8824 (pt0) cc_final: 0.8419 (pt0) REVERT: B 297 MET cc_start: 0.7619 (mtt) cc_final: 0.7320 (tpp) REVERT: B 586 ILE cc_start: 0.8466 (tt) cc_final: 0.8131 (tp) outliers start: 33 outliers final: 28 residues processed: 158 average time/residue: 0.1710 time to fit residues: 40.2296 Evaluate side-chains 154 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 95 VAL 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 148 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 175 LYS 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 303 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 TYR 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 233 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 562 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 41 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.215902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.165020 restraints weight = 11259.399| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.65 r_work: 0.3654 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9682 Z= 0.196 Angle : 0.555 14.877 13168 Z= 0.272 Chirality : 0.042 0.190 1606 Planarity : 0.003 0.027 1624 Dihedral : 4.496 30.455 1590 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.73 % Allowed : 25.29 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.61 (0.24), residues: 1152 helix: 2.66 (0.21), residues: 514 sheet: 1.32 (0.29), residues: 280 loop : -1.68 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 799 HIS 0.003 0.001 HIS B 492 PHE 0.027 0.002 PHE B 82 TYR 0.012 0.001 TYR B 173 ARG 0.004 0.000 ARG A 85 *********************** 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 162 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.044 Fit side-chains REVERT: A 61 ARG cc_start: 0.7018 (tpp80) cc_final: 0.6441 (mtm-85) REVERT: A 297 MET cc_start: 0.7648 (mtt) cc_final: 0.7152 (tpp) REVERT: A 562 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7204 (mm) REVERT: A 585 MET cc_start: 0.8418 (tmm) cc_final: 0.8143 (tmm) REVERT: B 61 ARG cc_start: 0.7032 (tpp80) cc_final: 0.6436 (mtm-85) REVERT: B 100 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8173 (ttm-80) REVERT: B 104 GLN cc_start: 0.8805 (pt0) cc_final: 0.8373 (pt0) REVERT: B 297 MET cc_start: 0.7674 (mtt) cc_final: 0.7277 (tpp) REVERT: B 586 ILE cc_start: 0.8333 (tt) cc_final: 0.8005 (tp) outliers start: 38 outliers final: 31 residues processed: 156 average time/residue: 0.1748 time to fit residues: 40.8621 Evaluate side-chains 156 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 95 VAL 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 174 PHE Chi-restraints excluded: chain A residue 175 LYS 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 303 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 812 LEU 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 174 PHE 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 289 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 498 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.0060 chunk 104 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 36 optimal weight: 5.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.215055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.165534 restraints weight = 11203.936| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.66 r_work: 0.3647 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9682 Z= 0.229 Angle : 0.561 13.869 13168 Z= 0.277 Chirality : 0.043 0.198 1606 Planarity : 0.003 0.028 1624 Dihedral : 4.442 28.578 1590 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.33 % Allowed : 25.20 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.62 (0.24), residues: 1152 helix: 2.70 (0.21), residues: 514 sheet: 1.26 (0.29), residues: 282 loop : -1.69 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 799 HIS 0.004 0.001 HIS B 55 PHE 0.023 0.002 PHE B 82 TYR 0.013 0.001 TYR B 173 ARG 0.005 0.000 ARG A 85 *********************** 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 157 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.088 Fit side-chains REVERT: A 61 ARG cc_start: 0.7011 (tpp80) cc_final: 0.6445 (mtm-85) REVERT: A 100 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8128 (ttm-80) REVERT: A 297 MET cc_start: 0.7684 (mtt) cc_final: 0.7191 (tpp) REVERT: A 562 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7236 (mm) REVERT: A 585 MET cc_start: 0.8425 (tmm) cc_final: 0.8138 (tmm) REVERT: B 61 ARG cc_start: 0.7041 (tpp80) cc_final: 0.6457 (mtm-85) REVERT: B 100 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8257 (ttm-80) REVERT: B 104 GLN cc_start: 0.8832 (pt0) cc_final: 0.8376 (pt0) REVERT: B 297 MET cc_start: 0.7698 (mtt) cc_final: 0.7258 (tpp) REVERT: B 586 ILE cc_start: 0.8355 (tt) cc_final: 0.8036 (tp) outliers start: 34 outliers final: 30 residues processed: 152 average time/residue: 0.1826 time to fit residues: 41.1233 Evaluate side-chains 152 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 95 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 174 PHE Chi-restraints excluded: chain A residue 175 LYS 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 303 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 751 CYS Chi-restraints excluded: chain A residue 812 LEU 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 289 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 498 SER 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 41 optimal weight: 8.9990 chunk 115 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.217130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.164009 restraints weight = 11370.010| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 4.30 r_work: 0.3673 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 0.039 9682 Z= 0.179 Angle : 0.546 13.813 13168 Z= 0.268 Chirality : 0.042 0.177 1606 Planarity : 0.003 0.028 1624 Dihedral : 4.262 26.889 1590 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.24 % Allowed : 25.20 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.63 (0.24), residues: 1152 helix: 2.69 (0.21), residues: 514 sheet: 1.29 (0.29), residues: 282 loop : -1.68 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 634 HIS 0.003 0.001 HIS B 55 PHE 0.022 0.001 PHE B 82 TYR 0.014 0.001 TYR A 308 ARG 0.004 0.000 ARG A 85 ********************** 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 165 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.022 Fit side-chains REVERT: A 61 ARG cc_start: 0.7035 (tpp80) cc_final: 0.6452 (mtm-85) REVERT: A 297 MET cc_start: 0.7647 (mtt) cc_final: 0.7123 (tpp) REVERT: A 562 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7149 (mm) REVERT: A 585 MET cc_start: 0.8381 (tmm) cc_final: 0.8098 (tmm) REVERT: B 61 ARG cc_start: 0.7016 (tpp80) cc_final: 0.6416 (mtm-85) REVERT: B 100 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8151 (ttm-80) REVERT: B 297 MET cc_start: 0.7674 (mtt) cc_final: 0.7205 (tpp) REVERT: B 586 ILE cc_start: 0.8236 (tt) cc_final: 0.7906 (tp) outliers start: 33 outliers final: 31 residues processed: 157 average time/residue: 0.2227 time to fit residues: 52.0911 Evaluate side-chains 160 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 95 VAL 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 174 PHE Chi-restraints excluded: chain A residue 175 LYS 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 303 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 TYR 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 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 289 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 498 SER 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 11 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4500 r_free = 0.4500 target = 0.216131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.164372 restraints weight = 11361.619| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.94 r_work: 0.3655 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9682 Z= 0.216 Angle : 0.556 13.495 13168 Z= 0.274 Chirality : 0.042 0.181 1606 Planarity : 0.003 0.027 1624 Dihedral : 4.209 26.113 1590 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.24 % Allowed : 25.69 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.65 (0.24), residues: 1152 helix: 2.73 (0.21), residues: 514 sheet: 1.27 (0.29), residues: 282 loop : -1.68 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 773 HIS 0.003 0.001 HIS A 492 PHE 0.023 0.002 PHE B 801 TYR 0.013 0.001 TYR B 173 ARG 0.004 0.000 ARG A 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5095.78 seconds wall clock time: 90 minutes 29.69 seconds (5429.69 seconds total)