Starting phenix.real_space_refine on Thu Jul 2 16:59:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dw3_27750/07_2026/8dw3_27750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dw3_27750/07_2026/8dw3_27750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dw3_27750/07_2026/8dw3_27750.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dw3_27750/07_2026/8dw3_27750.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dw3_27750/07_2026/8dw3_27750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dw3_27750/07_2026/8dw3_27750.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dw3_27750/07_2026/8dw3_27750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dw3_27750/07_2026/8dw3_27750.map" } resolution = 4.26 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= 0.002 sd= 0.019 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 33 5.16 5 C 5897 2.51 5 N 1564 2.21 5 O 1857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9351 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1140 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1521 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1624 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "H" Number of atoms: 1609 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 bond proxies already assigned to first conformer: 1646 Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1703 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.24, per 1000 atoms: 0.24 Number of scatterers: 9351 At special positions: 0 Unit cell: (82.062, 125.712, 174.6, 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 33 16.00 O 1857 8.00 N 1564 7.00 C 5897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.40 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 210 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 343 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 349.3 milliseconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 23 sheets defined 15.3% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 removed outlier: 3.928A pdb=" N GLU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.283A pdb=" N LEU A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.817A pdb=" N ASN A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 91 removed outlier: 3.930A pdb=" N LEU A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.747A pdb=" N GLU A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.610A pdb=" N LEU A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 removed outlier: 4.251A pdb=" N VAL A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.938A pdb=" N ILE A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 removed outlier: 4.275A pdb=" N ALA A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.543A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.558A pdb=" N ALA B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.803A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.789A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.869A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.640A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.606A pdb=" N LEU C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.724A pdb=" N SER D 31 " --> pdb=" O PRO D 28 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 199 through 203 removed outlier: 3.715A pdb=" N SER D 202 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.602A pdb=" N THR H 31 " --> pdb=" O GLY H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.947A pdb=" N GLN H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.989A pdb=" N VAL L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 134 Processing helix chain 'L' and resid 189 through 195 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.761A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.914A pdb=" N ARG C 24 " --> pdb=" O THR C 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 39 Processing sheet with id=AA6, first strand: chain 'C' and resid 34 through 39 Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 118 Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 150 Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.498A pdb=" N GLU D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY D 33 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 138 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 138 Processing sheet with id=AB5, first strand: chain 'D' and resid 165 through 168 removed outlier: 4.150A pdb=" N TYR D 208 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 2 through 5 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.734A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.734A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL H 108 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.630A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL H 185 " --> pdb=" O HIS H 168 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.121A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.570A pdb=" N THR L 108 " --> pdb=" O TYR L 92 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 120 through 124 removed outlier: 5.933A pdb=" N TYR L 179 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 151 through 156 336 hydrogen bonds defined for protein. 864 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: 1.32 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.50 - 0.77: 1 0.77 - 1.04: 0 1.04 - 1.31: 1548 1.31 - 1.58: 7967 1.58 - 1.84: 46 Bond restraints: 9562 Sorted by residual: bond pdb=" CG PRO D 28 " pdb=" CD PRO D 28 " ideal model delta sigma weight residual 1.503 0.505 0.998 3.40e-02 8.65e+02 8.62e+02 bond pdb=" CG PRO C 204 " pdb=" CD PRO C 204 " ideal model delta sigma weight residual 1.503 1.060 0.443 3.40e-02 8.65e+02 1.70e+02 bond pdb=" N PRO D 28 " pdb=" CD PRO D 28 " ideal model delta sigma weight residual 1.473 1.589 -0.116 1.40e-02 5.10e+03 6.84e+01 bond pdb=" CB PRO D 28 " pdb=" CG PRO D 28 " ideal model delta sigma weight residual 1.492 1.844 -0.352 5.00e-02 4.00e+02 4.95e+01 bond pdb=" N PRO C 204 " pdb=" CD PRO C 204 " ideal model delta sigma weight residual 1.473 1.569 -0.096 1.40e-02 5.10e+03 4.73e+01 ... (remaining 9557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.56: 12984 7.56 - 15.11: 14 15.11 - 22.67: 5 22.67 - 30.23: 0 30.23 - 37.79: 1 Bond angle restraints: 13004 Sorted by residual: angle pdb=" N PRO D 28 " pdb=" CD PRO D 28 " pdb=" CG PRO D 28 " ideal model delta sigma weight residual 103.20 65.41 37.79 1.50e+00 4.44e-01 6.35e+02 angle pdb=" N PRO C 204 " pdb=" CD PRO C 204 " pdb=" CG PRO C 204 " ideal model delta sigma weight residual 103.20 81.48 21.72 1.50e+00 4.44e-01 2.10e+02 angle pdb=" CA PRO C 204 " pdb=" N PRO C 204 " pdb=" CD PRO C 204 " ideal model delta sigma weight residual 112.00 94.26 17.74 1.40e+00 5.10e-01 1.61e+02 angle pdb=" CA PRO D 28 " pdb=" CB PRO D 28 " pdb=" CG PRO D 28 " ideal model delta sigma weight residual 104.50 81.83 22.67 1.90e+00 2.77e-01 1.42e+02 angle pdb=" CA PRO C 81 " pdb=" N PRO C 81 " pdb=" CD PRO C 81 " ideal model delta sigma weight residual 112.00 96.12 15.88 1.40e+00 5.10e-01 1.29e+02 ... (remaining 12999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4780 17.70 - 35.40: 700 35.40 - 53.10: 157 53.10 - 70.80: 21 70.80 - 88.50: 10 Dihedral angle restraints: 5668 sinusoidal: 2160 harmonic: 3508 Sorted by residual: dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 210 " pdb=" CB CYS D 210 " ideal model delta sinusoidal sigma weight residual -86.00 -167.97 81.97 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 16.91 76.09 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS C 134 " pdb=" SG CYS C 134 " pdb=" SG CYS C 194 " pdb=" CB CYS C 194 " ideal model delta sinusoidal sigma weight residual -86.00 -161.05 75.05 1 1.00e+01 1.00e-02 7.12e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1453 0.131 - 0.263: 12 0.263 - 0.394: 2 0.394 - 0.525: 0 0.525 - 0.657: 1 Chirality restraints: 1468 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.77e+02 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA TRP D 50 " pdb=" N TRP D 50 " pdb=" C TRP D 50 " pdb=" CB TRP D 50 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1465 not shown) Planarity restraints: 1671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.081 2.00e-02 2.50e+03 6.71e-02 5.62e+01 pdb=" C7 NAG E 1 " 0.020 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.061 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.108 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 160 " 0.085 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO D 161 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 50 " 0.034 2.00e-02 2.50e+03 3.08e-02 2.37e+01 pdb=" CG TRP D 50 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP D 50 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP D 50 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 50 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 50 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 50 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP D 50 " 0.001 2.00e-02 2.50e+03 ... (remaining 1668 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 233 2.66 - 3.22: 8587 3.22 - 3.78: 13725 3.78 - 4.34: 17656 4.34 - 4.90: 29133 Nonbonded interactions: 69334 Sorted by model distance: nonbonded pdb=" OG1 THR B 345 " pdb=" OG SER D 109 " model vdw 2.105 3.040 nonbonded pdb=" O ILE C 106 " pdb=" OH TYR C 140 " model vdw 2.176 3.040 nonbonded pdb=" O SER C 121 " pdb=" NE2 GLN C 124 " model vdw 2.186 3.120 nonbonded pdb=" OG SER B 383 " pdb=" OG SER H 100 " model vdw 2.198 3.040 nonbonded pdb=" OG SER D 202 " pdb=" OE1 GLN D 206 " model vdw 2.204 3.040 ... (remaining 69329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ through 20 or resid 23 or resid 26 through 27 or resid 29 through 31 or resid 3 \ 4 through 43 or resid 45 or resid 47 through 50 or resid 52 through 53 or resid \ 55 or resid 58 or resid 60 through 77 or resid 79 or resid 82 through 83 or resi \ d 85 through 91 or resid 94 or resid 97 through 99 or resid 101 through 213)) selection = (chain 'L' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ through 20 or resid 23 or resid 26 through 27 or resid 29 or resid 32 through 3 \ 3 or resid 39 through 48 or resid 50 or resid 52 through 55 or resid 57 through \ 58 or resid 60 or resid 63 or resid 65 through 82 or resid 84 or resid 87 throug \ h 88 or resid 90 through 96 or resid 100 or resid 103 through 105 or resid 107 t \ hrough 219)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.640 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 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 : 0.014 0.998 9578 Z= 0.646 Angle : 0.965 37.787 13037 Z= 0.532 Chirality : 0.051 0.657 1468 Planarity : 0.008 0.122 1670 Dihedral : 17.027 88.502 3398 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.21 % Rotamer: Outliers : 0.10 % Allowed : 37.69 % Favored : 62.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.24), residues: 1209 helix: -0.33 (0.49), residues: 104 sheet: 0.37 (0.27), residues: 418 loop : -1.29 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 148 TYR 0.041 0.001 TYR L 102 PHE 0.025 0.001 PHE L 145 TRP 0.082 0.003 TRP D 50 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.01266 / 0.40 ( 9562) covalent geometry : angle 0.94946 / 0.53 (13004) SS BOND : bond 0.10592 / 8.27 ( 12) SS BOND : angle 3.49234 / 1.68 ( 24) hydrogen bonds : bond 0.14673 / 9.95 ( 314) hydrogen bonds : angle 6.46055 / 4.63 ( 864) Misc. bond : bond 0.46470 / 29.04 ( 1) link_BETA1-4 : bond 0.00339 / 0.20 ( 2) link_BETA1-4 : angle 2.06847 / 1.19 ( 6) link_NAG-ASN : bond 0.00913 / 0.57 ( 1) link_NAG-ASN : angle 6.00156 / 2.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8274 (mp) cc_final: 0.7734 (tp) REVERT: B 489 TYR cc_start: 0.6882 (m-80) cc_final: 0.6449 (m-80) REVERT: C 117 ILE cc_start: 0.9102 (tt) cc_final: 0.8880 (tt) REVERT: C 154 LEU cc_start: 0.9124 (tp) cc_final: 0.8874 (pt) REVERT: D 48 MET cc_start: 0.6484 (mmm) cc_final: 0.6169 (tpp) REVERT: D 138 LEU cc_start: 0.7749 (tp) cc_final: 0.7006 (mp) REVERT: D 168 TRP cc_start: 0.7187 (m100) cc_final: 0.6603 (m100) REVERT: D 210 CYS cc_start: 0.4075 (t) cc_final: 0.2355 (t) REVERT: H 158 TRP cc_start: 0.7154 (m100) cc_final: 0.6662 (m100) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 0.1008 time to fit residues: 28.7847 Evaluate side-chains 128 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN D 218 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 ASN ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 172 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.067767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.052119 restraints weight = 70838.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053754 restraints weight = 39474.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054883 restraints weight = 26191.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.055660 restraints weight = 19298.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.056205 restraints weight = 15449.081| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 9578 Z= 0.293 Angle : 0.801 8.718 13037 Z= 0.409 Chirality : 0.047 0.178 1468 Planarity : 0.006 0.087 1670 Dihedral : 5.283 30.579 1311 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.78 % Favored : 92.14 % Rotamer: Outliers : 0.48 % Allowed : 7.36 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.24), residues: 1209 helix: -0.52 (0.46), residues: 118 sheet: 0.08 (0.26), residues: 437 loop : -1.42 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 38 TYR 0.023 0.003 TYR L 98 PHE 0.027 0.003 PHE C 98 TRP 0.031 0.003 TRP D 50 HIS 0.011 0.002 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.29 ( 9562) covalent geometry : angle 0.79520 / 0.41 (13004) SS BOND : bond 0.01481 / 0.82 ( 12) SS BOND : angle 1.88816 / 0.99 ( 24) hydrogen bonds : bond 0.03596 / 2.49 ( 314) hydrogen bonds : angle 5.75632 / 4.19 ( 864) Misc. bond : bond 0.00559 / 0.35 ( 1) link_BETA1-4 : bond 0.01203 / 0.72 ( 2) link_BETA1-4 : angle 2.23113 / 1.05 ( 6) link_NAG-ASN : bond 0.03107 / 1.94 ( 1) link_NAG-ASN : angle 2.69132 / 1.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9477 (mp) cc_final: 0.9115 (tp) REVERT: B 386 LYS cc_start: 0.9076 (mtpp) cc_final: 0.8766 (mtmt) REVERT: B 390 LEU cc_start: 0.8650 (pp) cc_final: 0.8393 (pp) REVERT: B 414 GLN cc_start: 0.8241 (tt0) cc_final: 0.7837 (tm-30) REVERT: B 456 PHE cc_start: 0.6724 (t80) cc_final: 0.5783 (t80) REVERT: B 458 LYS cc_start: 0.8575 (mttt) cc_final: 0.8007 (mmtm) REVERT: B 489 TYR cc_start: 0.7252 (m-80) cc_final: 0.7024 (m-80) REVERT: B 516 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7705 (tm-30) REVERT: C 118 PHE cc_start: 0.8243 (m-80) cc_final: 0.7499 (m-80) REVERT: D 48 MET cc_start: 0.8731 (mmm) cc_final: 0.8194 (tpp) REVERT: D 87 ARG cc_start: 0.8768 (mpp-170) cc_final: 0.8319 (mtt90) REVERT: D 94 TYR cc_start: 0.9030 (m-10) cc_final: 0.8623 (m-80) REVERT: D 108 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8751 (mp0) REVERT: D 168 TRP cc_start: 0.7886 (m100) cc_final: 0.6908 (m100) REVERT: D 210 CYS cc_start: 0.8012 (t) cc_final: 0.5979 (t) REVERT: H 37 VAL cc_start: 0.9604 (t) cc_final: 0.9302 (p) REVERT: H 48 MET cc_start: 0.8858 (mpp) cc_final: 0.8578 (mpp) REVERT: H 83 TRP cc_start: 0.8042 (m100) cc_final: 0.7323 (m100) REVERT: H 149 TYR cc_start: 0.5466 (p90) cc_final: 0.5168 (p90) REVERT: H 158 TRP cc_start: 0.7616 (m100) cc_final: 0.7175 (m100) outliers start: 5 outliers final: 2 residues processed: 155 average time/residue: 0.0862 time to fit residues: 19.6579 Evaluate side-chains 93 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 218 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 GLN ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.065868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050673 restraints weight = 69212.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.052229 restraints weight = 39217.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053278 restraints weight = 26305.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.054025 restraints weight = 19713.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054525 restraints weight = 15969.483| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9578 Z= 0.278 Angle : 0.741 9.417 13037 Z= 0.376 Chirality : 0.046 0.167 1468 Planarity : 0.006 0.063 1670 Dihedral : 5.251 32.387 1311 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.95 % Favored : 92.97 % Rotamer: Outliers : 0.29 % Allowed : 6.10 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.24), residues: 1209 helix: -0.58 (0.45), residues: 118 sheet: -0.12 (0.25), residues: 424 loop : -1.50 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 23 TYR 0.022 0.002 TYR D 190 PHE 0.018 0.002 PHE B 429 TRP 0.026 0.002 TRP D 105 HIS 0.010 0.002 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.28 ( 9562) covalent geometry : angle 0.73370 / 0.37 (13004) SS BOND : bond 0.00599 / 0.38 ( 12) SS BOND : angle 1.83273 / 0.94 ( 24) hydrogen bonds : bond 0.03478 / 2.38 ( 314) hydrogen bonds : angle 5.71299 / 4.15 ( 864) Misc. bond : bond 0.00252 / 0.16 ( 1) link_BETA1-4 : bond 0.00221 / 0.14 ( 2) link_BETA1-4 : angle 2.38035 / 1.11 ( 6) link_NAG-ASN : bond 0.00429 / 0.27 ( 1) link_NAG-ASN : angle 3.88827 / 2.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 386 LYS cc_start: 0.8999 (mtpp) cc_final: 0.8763 (mtmm) REVERT: B 390 LEU cc_start: 0.8530 (pp) cc_final: 0.8246 (pp) REVERT: B 420 ASP cc_start: 0.9000 (t0) cc_final: 0.8794 (t0) REVERT: B 458 LYS cc_start: 0.8439 (mppt) cc_final: 0.8075 (mmtt) REVERT: B 489 TYR cc_start: 0.7446 (m-80) cc_final: 0.7023 (m-80) REVERT: B 516 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 168 TRP cc_start: 0.7916 (m100) cc_final: 0.6731 (m100) REVERT: D 210 CYS cc_start: 0.7867 (t) cc_final: 0.6332 (t) REVERT: H 10 GLU cc_start: 0.8055 (tp30) cc_final: 0.7608 (tp30) REVERT: H 83 TRP cc_start: 0.8123 (m100) cc_final: 0.7499 (m100) REVERT: H 158 TRP cc_start: 0.7670 (m100) cc_final: 0.7259 (m100) REVERT: L 102 TYR cc_start: 0.6363 (OUTLIER) cc_final: 0.5532 (m-80) REVERT: L 130 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8104 (tp-100) outliers start: 3 outliers final: 0 residues processed: 134 average time/residue: 0.0867 time to fit residues: 17.0031 Evaluate side-chains 83 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 115 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.052044 restraints weight = 70845.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.053551 restraints weight = 36861.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054899 restraints weight = 22398.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.055046 restraints weight = 17254.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055147 restraints weight = 14744.816| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9578 Z= 0.186 Angle : 0.677 9.966 13037 Z= 0.336 Chirality : 0.045 0.206 1468 Planarity : 0.005 0.054 1670 Dihedral : 5.009 30.615 1311 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.78 % Favored : 93.13 % Rotamer: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.24), residues: 1209 helix: -0.35 (0.45), residues: 119 sheet: -0.13 (0.25), residues: 431 loop : -1.37 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 98 TYR 0.022 0.002 TYR H 180 PHE 0.015 0.002 PHE B 347 TRP 0.022 0.002 TRP D 105 HIS 0.007 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 9562) covalent geometry : angle 0.66575 / 0.33 (13004) SS BOND : bond 0.00468 / 0.31 ( 12) SS BOND : angle 1.58503 / 0.83 ( 24) hydrogen bonds : bond 0.02909 / 2.01 ( 314) hydrogen bonds : angle 5.53867 / 4.00 ( 864) Misc. bond : bond 0.00053 / 0.03 ( 1) link_BETA1-4 : bond 0.00655 / 0.41 ( 2) link_BETA1-4 : angle 2.55520 / 1.28 ( 6) link_NAG-ASN : bond 0.01332 / 0.83 ( 1) link_NAG-ASN : angle 6.05703 / 3.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9401 (tp30) cc_final: 0.8683 (pt0) REVERT: B 390 LEU cc_start: 0.8594 (pp) cc_final: 0.8348 (pp) REVERT: B 458 LYS cc_start: 0.8417 (mppt) cc_final: 0.8064 (mmtt) REVERT: B 516 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7752 (tm-30) REVERT: D 48 MET cc_start: 0.8400 (mmt) cc_final: 0.7996 (mtt) REVERT: D 168 TRP cc_start: 0.7949 (m100) cc_final: 0.6779 (m100) REVERT: D 206 GLN cc_start: 0.5184 (OUTLIER) cc_final: 0.4881 (pp30) REVERT: D 210 CYS cc_start: 0.8052 (t) cc_final: 0.6439 (t) REVERT: H 10 GLU cc_start: 0.8202 (tp30) cc_final: 0.7694 (tp30) REVERT: H 83 TRP cc_start: 0.8187 (m100) cc_final: 0.7138 (m100) REVERT: H 158 TRP cc_start: 0.7697 (m100) cc_final: 0.7287 (m100) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.0834 time to fit residues: 15.9205 Evaluate side-chains 84 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.0670 chunk 18 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 overall best weight: 2.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN C 38 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN H 82 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.066811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.051732 restraints weight = 57998.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.053282 restraints weight = 33562.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.054331 restraints weight = 22598.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055013 restraints weight = 16984.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.055520 restraints weight = 13914.051| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9578 Z= 0.144 Angle : 0.651 10.479 13037 Z= 0.320 Chirality : 0.045 0.154 1468 Planarity : 0.004 0.052 1670 Dihedral : 4.832 31.690 1311 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.70 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.25), residues: 1209 helix: 0.03 (0.49), residues: 113 sheet: -0.03 (0.25), residues: 427 loop : -1.31 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 98 TYR 0.013 0.001 TYR B 396 PHE 0.014 0.002 PHE D 114 TRP 0.017 0.002 TRP D 105 HIS 0.004 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9562) covalent geometry : angle 0.63601 / 0.32 (13004) SS BOND : bond 0.00367 / 0.24 ( 12) SS BOND : angle 1.43898 / 0.81 ( 24) hydrogen bonds : bond 0.02698 / 1.86 ( 314) hydrogen bonds : angle 5.39551 / 3.86 ( 864) Misc. bond : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : bond 0.00597 / 0.37 ( 2) link_BETA1-4 : angle 2.73007 / 1.40 ( 6) link_NAG-ASN : bond 0.00883 / 0.55 ( 1) link_NAG-ASN : angle 7.51331 / 4.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9379 (tp30) cc_final: 0.8691 (pt0) REVERT: B 390 LEU cc_start: 0.8666 (pp) cc_final: 0.8278 (pp) REVERT: B 456 PHE cc_start: 0.7015 (t80) cc_final: 0.6642 (t80) REVERT: B 458 LYS cc_start: 0.8368 (mppt) cc_final: 0.7950 (mmtt) REVERT: B 516 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7671 (tm-30) REVERT: D 48 MET cc_start: 0.8407 (mmt) cc_final: 0.8147 (mtt) REVERT: D 168 TRP cc_start: 0.7951 (m100) cc_final: 0.6885 (m100) REVERT: D 210 CYS cc_start: 0.7826 (t) cc_final: 0.6098 (t) REVERT: H 10 GLU cc_start: 0.8100 (tp30) cc_final: 0.7649 (tp30) REVERT: H 158 TRP cc_start: 0.7703 (m100) cc_final: 0.7309 (m100) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0862 time to fit residues: 15.8919 Evaluate side-chains 87 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 0.0170 chunk 66 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.066994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.052028 restraints weight = 58503.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053565 restraints weight = 34023.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054572 restraints weight = 22874.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055288 restraints weight = 17270.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055763 restraints weight = 14085.503| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9578 Z= 0.138 Angle : 0.654 10.872 13037 Z= 0.317 Chirality : 0.044 0.155 1468 Planarity : 0.004 0.052 1670 Dihedral : 4.735 33.152 1311 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.62 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.25), residues: 1209 helix: 0.07 (0.49), residues: 113 sheet: 0.01 (0.25), residues: 446 loop : -1.28 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 67 TYR 0.020 0.001 TYR H 52 PHE 0.015 0.002 PHE H 170 TRP 0.015 0.001 TRP H 33 HIS 0.004 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9562) covalent geometry : angle 0.63443 / 0.31 (13004) SS BOND : bond 0.00322 / 0.22 ( 12) SS BOND : angle 1.38847 / 0.77 ( 24) hydrogen bonds : bond 0.02678 / 1.85 ( 314) hydrogen bonds : angle 5.29113 / 3.80 ( 864) Misc. bond : bond 0.00028 / 0.02 ( 1) link_BETA1-4 : bond 0.00518 / 0.32 ( 2) link_BETA1-4 : angle 2.81428 / 1.45 ( 6) link_NAG-ASN : bond 0.00483 / 0.30 ( 1) link_NAG-ASN : angle 9.01185 / 4.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9364 (tp30) cc_final: 0.8678 (pt0) REVERT: B 390 LEU cc_start: 0.8634 (pp) cc_final: 0.8292 (pp) REVERT: B 456 PHE cc_start: 0.7067 (t80) cc_final: 0.6761 (t80) REVERT: B 458 LYS cc_start: 0.8522 (mppt) cc_final: 0.8155 (mmtt) REVERT: D 81 MET cc_start: 0.8927 (tmm) cc_final: 0.8578 (tmm) REVERT: D 168 TRP cc_start: 0.7888 (m100) cc_final: 0.6804 (m100) REVERT: D 210 CYS cc_start: 0.7762 (t) cc_final: 0.5739 (t) REVERT: H 10 GLU cc_start: 0.8192 (tp30) cc_final: 0.7694 (tp30) REVERT: H 16 GLU cc_start: 0.8949 (mp0) cc_final: 0.8646 (mp0) REVERT: H 83 TRP cc_start: 0.7770 (m100) cc_final: 0.6846 (m100) REVERT: H 158 TRP cc_start: 0.7703 (m100) cc_final: 0.7327 (m100) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0754 time to fit residues: 14.9652 Evaluate side-chains 91 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 74 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.050104 restraints weight = 68603.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.051659 restraints weight = 38952.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052723 restraints weight = 25915.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053464 restraints weight = 19223.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.053958 restraints weight = 15471.074| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9578 Z= 0.215 Angle : 0.692 11.447 13037 Z= 0.345 Chirality : 0.045 0.152 1468 Planarity : 0.005 0.056 1670 Dihedral : 4.993 28.640 1311 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.19 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.24), residues: 1209 helix: 0.06 (0.48), residues: 113 sheet: -0.03 (0.25), residues: 428 loop : -1.39 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 38 TYR 0.024 0.002 TYR H 180 PHE 0.018 0.002 PHE H 170 TRP 0.016 0.002 TRP D 50 HIS 0.008 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 ( 9562) covalent geometry : angle 0.68107 / 0.34 (13004) SS BOND : bond 0.00689 / 0.34 ( 12) SS BOND : angle 1.64176 / 0.82 ( 24) hydrogen bonds : bond 0.03053 / 2.10 ( 314) hydrogen bonds : angle 5.47977 / 3.94 ( 864) Misc. bond : bond 0.00055 / 0.03 ( 1) link_BETA1-4 : bond 0.00406 / 0.25 ( 2) link_BETA1-4 : angle 2.49671 / 1.31 ( 6) link_NAG-ASN : bond 0.00393 / 0.25 ( 1) link_NAG-ASN : angle 5.89952 / 3.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9341 (tp30) cc_final: 0.8662 (pt0) REVERT: A 102 ASN cc_start: 0.8789 (p0) cc_final: 0.8565 (p0) REVERT: B 390 LEU cc_start: 0.8707 (pp) cc_final: 0.8367 (pp) REVERT: B 456 PHE cc_start: 0.7373 (t80) cc_final: 0.6689 (t80) REVERT: B 458 LYS cc_start: 0.8589 (mppt) cc_final: 0.8137 (mmtt) REVERT: D 3 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7942 (tm-30) REVERT: D 81 MET cc_start: 0.8892 (tmm) cc_final: 0.8639 (tmm) REVERT: D 168 TRP cc_start: 0.7854 (m100) cc_final: 0.6702 (m100) REVERT: D 210 CYS cc_start: 0.7930 (t) cc_final: 0.5970 (t) REVERT: H 10 GLU cc_start: 0.8234 (tp30) cc_final: 0.7727 (tp30) REVERT: H 83 TRP cc_start: 0.7986 (m100) cc_final: 0.7091 (m100) REVERT: H 158 TRP cc_start: 0.7726 (m100) cc_final: 0.7355 (m100) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0744 time to fit residues: 13.1891 Evaluate side-chains 83 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 49 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 HIS ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** 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 = 0.3432 r_free = 0.3432 target = 0.065572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.050480 restraints weight = 70084.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.052079 restraints weight = 38946.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.053163 restraints weight = 25718.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.053921 restraints weight = 18989.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054398 restraints weight = 15178.217| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9578 Z= 0.169 Angle : 0.688 13.570 13037 Z= 0.334 Chirality : 0.045 0.175 1468 Planarity : 0.004 0.056 1670 Dihedral : 4.952 35.388 1311 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.20 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.24), residues: 1209 helix: -0.05 (0.48), residues: 113 sheet: -0.02 (0.25), residues: 428 loop : -1.32 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.022 0.002 TYR D 95 PHE 0.016 0.002 PHE C 72 TRP 0.016 0.002 TRP H 33 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 9562) covalent geometry : angle 0.65727 / 0.33 (13004) SS BOND : bond 0.00420 / 0.27 ( 12) SS BOND : angle 1.38606 / 0.74 ( 24) hydrogen bonds : bond 0.02825 / 1.94 ( 314) hydrogen bonds : angle 5.38803 / 3.86 ( 864) Misc. bond : bond 0.00049 / 0.03 ( 1) link_BETA1-4 : bond 0.00801 / 0.49 ( 2) link_BETA1-4 : angle 3.07407 / 1.62 ( 6) link_NAG-ASN : bond 0.00352 / 0.22 ( 1) link_NAG-ASN : angle 12.19425 / 6.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.9435 (tp30) cc_final: 0.8767 (pt0) REVERT: A 102 ASN cc_start: 0.8857 (p0) cc_final: 0.8635 (p0) REVERT: B 386 LYS cc_start: 0.9043 (mtmt) cc_final: 0.8489 (ptmt) REVERT: B 390 LEU cc_start: 0.8647 (pp) cc_final: 0.8293 (pp) REVERT: B 456 PHE cc_start: 0.7392 (t80) cc_final: 0.6734 (t80) REVERT: B 458 LYS cc_start: 0.8471 (mppt) cc_final: 0.8040 (mmtt) REVERT: D 3 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7974 (tm-30) REVERT: D 168 TRP cc_start: 0.7886 (m100) cc_final: 0.6891 (m100) REVERT: D 210 CYS cc_start: 0.7928 (t) cc_final: 0.5852 (t) REVERT: H 10 GLU cc_start: 0.8300 (tp30) cc_final: 0.7759 (tp30) REVERT: H 40 MET cc_start: 0.8663 (mmm) cc_final: 0.8327 (mmt) REVERT: H 83 TRP cc_start: 0.7999 (m100) cc_final: 0.7137 (m100) REVERT: H 158 TRP cc_start: 0.7727 (m100) cc_final: 0.7369 (m100) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0690 time to fit residues: 11.6239 Evaluate side-chains 81 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.064976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.049964 restraints weight = 69308.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.051568 restraints weight = 38712.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052667 restraints weight = 25660.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053414 restraints weight = 18966.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053933 restraints weight = 15202.988| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9578 Z= 0.185 Angle : 0.699 12.015 13037 Z= 0.342 Chirality : 0.045 0.152 1468 Planarity : 0.004 0.058 1670 Dihedral : 5.003 33.678 1311 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.24), residues: 1209 helix: -0.03 (0.48), residues: 113 sheet: -0.04 (0.25), residues: 428 loop : -1.30 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.033 0.002 TYR L 102 PHE 0.016 0.002 PHE C 72 TRP 0.016 0.002 TRP D 105 HIS 0.006 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 9562) covalent geometry : angle 0.67625 / 0.34 (13004) SS BOND : bond 0.00578 / 0.35 ( 12) SS BOND : angle 1.55333 / 0.83 ( 24) hydrogen bonds : bond 0.02891 / 1.99 ( 314) hydrogen bonds : angle 5.39998 / 3.87 ( 864) Misc. bond : bond 0.00061 / 0.04 ( 1) link_BETA1-4 : bond 0.00857 / 0.53 ( 2) link_BETA1-4 : angle 2.82359 / 1.48 ( 6) link_NAG-ASN : bond 0.00156 / 0.10 ( 1) link_NAG-ASN : angle 10.29278 / 4.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8839 (p0) cc_final: 0.8603 (p0) REVERT: B 386 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8659 (ptpt) REVERT: B 390 LEU cc_start: 0.8643 (pp) cc_final: 0.8306 (pp) REVERT: B 458 LYS cc_start: 0.8510 (mppt) cc_final: 0.8200 (mmtt) REVERT: D 3 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7967 (tm-30) REVERT: D 158 ASP cc_start: 0.8601 (m-30) cc_final: 0.8398 (m-30) REVERT: D 168 TRP cc_start: 0.7849 (m100) cc_final: 0.6794 (m100) REVERT: D 210 CYS cc_start: 0.7812 (t) cc_final: 0.5775 (t) REVERT: H 10 GLU cc_start: 0.8241 (tp30) cc_final: 0.7735 (tp30) REVERT: H 83 TRP cc_start: 0.7969 (m100) cc_final: 0.7173 (m100) REVERT: H 158 TRP cc_start: 0.7722 (m100) cc_final: 0.7376 (m100) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0721 time to fit residues: 11.8568 Evaluate side-chains 80 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 0.0270 chunk 108 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 1 optimal weight: 0.2980 chunk 26 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 HIS ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.067204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.051957 restraints weight = 68711.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053631 restraints weight = 37480.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054766 restraints weight = 24500.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055538 restraints weight = 17974.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.056064 restraints weight = 14366.840| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9578 Z= 0.116 Angle : 0.698 11.713 13037 Z= 0.334 Chirality : 0.046 0.226 1468 Planarity : 0.004 0.052 1670 Dihedral : 4.696 33.226 1311 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.25), residues: 1209 helix: 0.28 (0.51), residues: 106 sheet: 0.08 (0.25), residues: 437 loop : -1.17 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 59 TYR 0.024 0.002 TYR H 52 PHE 0.013 0.001 PHE C 72 TRP 0.024 0.002 TRP H 47 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9562) covalent geometry : angle 0.67078 / 0.33 (13004) SS BOND : bond 0.00455 / 0.31 ( 12) SS BOND : angle 2.83802 / 1.57 ( 24) hydrogen bonds : bond 0.02608 / 1.82 ( 314) hydrogen bonds : angle 5.14602 / 3.66 ( 864) Misc. bond : bond 0.00002 / 0.00 ( 1) link_BETA1-4 : bond 0.00949 / 0.58 ( 2) link_BETA1-4 : angle 2.93155 / 1.48 ( 6) link_NAG-ASN : bond 0.00028 / 0.02 ( 1) link_NAG-ASN : angle 9.14292 / 4.49 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8870 (p0) cc_final: 0.8628 (p0) REVERT: B 386 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8654 (ptpt) REVERT: B 390 LEU cc_start: 0.8601 (pp) cc_final: 0.8262 (pp) REVERT: B 456 PHE cc_start: 0.7379 (t80) cc_final: 0.6995 (t80) REVERT: B 458 LYS cc_start: 0.8548 (mppt) cc_final: 0.8095 (mmtp) REVERT: D 3 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8079 (tm-30) REVERT: D 168 TRP cc_start: 0.7736 (m100) cc_final: 0.6825 (m100) REVERT: D 210 CYS cc_start: 0.7766 (t) cc_final: 0.5438 (t) REVERT: H 10 GLU cc_start: 0.8375 (tp30) cc_final: 0.7901 (tp30) REVERT: H 12 LYS cc_start: 0.8026 (tptp) cc_final: 0.7685 (tptt) REVERT: H 16 GLU cc_start: 0.9000 (mp0) cc_final: 0.8727 (mp0) REVERT: H 83 TRP cc_start: 0.7894 (m100) cc_final: 0.7055 (m100) REVERT: H 158 TRP cc_start: 0.7697 (m100) cc_final: 0.7346 (m100) REVERT: L 124 PHE cc_start: 0.7883 (m-80) cc_final: 0.7047 (m-80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0665 time to fit residues: 13.0032 Evaluate side-chains 89 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 37 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** 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 = 0.3444 r_free = 0.3444 target = 0.065959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.051070 restraints weight = 67333.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.052675 restraints weight = 37396.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.053749 restraints weight = 24669.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054515 restraints weight = 18220.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055018 restraints weight = 14577.387| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9578 Z= 0.157 Angle : 0.708 15.432 13037 Z= 0.346 Chirality : 0.046 0.245 1468 Planarity : 0.004 0.056 1670 Dihedral : 4.753 32.423 1311 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.20 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.24), residues: 1209 helix: -0.07 (0.50), residues: 107 sheet: 0.11 (0.25), residues: 426 loop : -1.19 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 59 TYR 0.021 0.002 TYR L 102 PHE 0.014 0.002 PHE C 72 TRP 0.019 0.002 TRP H 47 HIS 0.006 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 9562) covalent geometry : angle 0.68687 / 0.34 (13004) SS BOND : bond 0.00529 / 0.32 ( 12) SS BOND : angle 2.35841 / 1.38 ( 24) hydrogen bonds : bond 0.02863 / 2.00 ( 314) hydrogen bonds : angle 5.25073 / 3.76 ( 864) Misc. bond : bond 0.00047 / 0.03 ( 1) link_BETA1-4 : bond 0.00605 / 0.36 ( 2) link_BETA1-4 : angle 2.83700 / 1.49 ( 6) link_NAG-ASN : bond 0.00159 / 0.10 ( 1) link_NAG-ASN : angle 8.35973 / 4.12 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1754.13 seconds wall clock time: 31 minutes 8.10 seconds (1868.10 seconds total)