Starting phenix.real_space_refine on Fri Oct 10 18:24:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpy_37726/10_2025/8wpy_37726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpy_37726/10_2025/8wpy_37726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wpy_37726/10_2025/8wpy_37726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpy_37726/10_2025/8wpy_37726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wpy_37726/10_2025/8wpy_37726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpy_37726/10_2025/8wpy_37726.map" } resolution = 3.02 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= 0.001 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 34 5.16 5 C 5312 2.51 5 N 1397 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8408 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "B" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "C" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 926 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "R" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.22, per 1000 atoms: 0.26 Number of scatterers: 8408 At special positions: 0 Unit cell: (86.7, 100.3, 150.45, 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 34 16.00 O 1665 8.00 N 1397 7.00 C 5312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 210 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " BETA1-6 " NAG E 1 " - " FUC E 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG E 1 " - " ASN R 343 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 409.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 25 sheets defined 8.8% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.573A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.931A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.610A pdb=" N SER A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.812A pdb=" N LEU B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.801A pdb=" N GLU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.629A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 90' Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.145A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.776A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.041A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.565A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 removed outlier: 4.086A pdb=" N ASN R 370 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 386 through 390 removed outlier: 3.611A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.266A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.696A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.977A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.291A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138 removed outlier: 3.642A pdb=" N SER A 194 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 138 removed outlier: 3.642A pdb=" N SER A 194 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168 removed outlier: 4.739A pdb=" N TYR A 208 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 223 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 212 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 221 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.689A pdb=" N SER B 7 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 12.376A pdb=" N CYS B 23 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 11.549A pdb=" N THR B 75 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N ALA B 25 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 11.704A pdb=" N THR B 73 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N GLN B 27 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP B 71 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY B 69 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 7.048A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 133 removed outlier: 3.776A pdb=" N VAL B 132 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 178 " --> pdb=" O GLN B 160 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 160 " --> pdb=" O THR B 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.518A pdb=" N LYS B 145 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR B 192 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 207 " --> pdb=" O CYS B 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.150A pdb=" N TYR C 33 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.607A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS D 23 " --> pdb=" O PHE D 71 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.608A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.504A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.009A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.684A pdb=" N CYS H 95 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TRP H 110 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG H 97 " --> pdb=" O ASP H 108 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR H 104 " --> pdb=" O SER H 101 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.634A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.588A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.219A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 93 through 94 removed outlier: 3.558A pdb=" N ASN R 394 " --> pdb=" O GLU R 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'R' and resid 473 through 474 317 hydrogen bonds defined for protein. 768 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: 1.38 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2674 1.34 - 1.46: 2262 1.46 - 1.58: 3631 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 8611 Sorted by residual: bond pdb=" C TYR B 140 " pdb=" N PRO B 141 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.12e-02 7.97e+03 4.26e+00 bond pdb=" CA GLY B 69 " pdb=" C GLY B 69 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.94e+00 bond pdb=" N GLY B 69 " pdb=" CA GLY B 69 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.81e+00 bond pdb=" C1 FUC E 4 " pdb=" C2 FUC E 4 " ideal model delta sigma weight residual 1.528 1.554 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.42e+00 ... (remaining 8606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 11389 1.27 - 2.53: 253 2.53 - 3.80: 50 3.80 - 5.07: 12 5.07 - 6.33: 5 Bond angle restraints: 11709 Sorted by residual: angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 113.10 110.08 3.02 9.70e-01 1.06e+00 9.72e+00 angle pdb=" C ALA L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.84 -4.30 1.91e+00 2.74e-01 5.06e+00 angle pdb=" C3 BMA E 3 " pdb=" C2 BMA E 3 " pdb=" O2 BMA E 3 " ideal model delta sigma weight residual 112.95 106.62 6.33 3.00e+00 1.11e-01 4.46e+00 angle pdb=" N ILE D 29 " pdb=" CA ILE D 29 " pdb=" C ILE D 29 " ideal model delta sigma weight residual 111.88 109.66 2.22 1.06e+00 8.90e-01 4.40e+00 angle pdb=" C GLY B 51 " pdb=" N ALA B 52 " pdb=" CA ALA B 52 " ideal model delta sigma weight residual 121.54 125.45 -3.91 1.91e+00 2.74e-01 4.18e+00 ... (remaining 11704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 5029 23.80 - 47.59: 82 47.59 - 71.39: 7 71.39 - 95.19: 8 95.19 - 118.98: 7 Dihedral angle restraints: 5133 sinusoidal: 2002 harmonic: 3131 Sorted by residual: dihedral pdb=" C2 FUC E 4 " pdb=" C1 FUC E 4 " pdb=" O5 FUC E 4 " pdb=" C5 FUC E 4 " ideal model delta sinusoidal sigma weight residual 57.68 -61.30 118.98 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.83 107.54 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C3 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 47.62 -57.94 105.56 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 5130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1121 0.056 - 0.112: 152 0.112 - 0.168: 23 0.168 - 0.224: 0 0.224 - 0.280: 1 Chirality restraints: 1297 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C2 BMA E 3 " pdb=" C1 BMA E 3 " pdb=" C3 BMA E 3 " pdb=" O2 BMA E 3 " both_signs ideal model delta sigma weight residual False 2.47 2.62 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA VAL A 37 " pdb=" N VAL A 37 " pdb=" C VAL A 37 " pdb=" CB VAL A 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1294 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 93 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO D 94 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 94 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 94 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 99 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO C 100 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 100 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 100 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 43 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO D 44 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 44 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 44 " -0.017 5.00e-02 4.00e+02 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 641 2.75 - 3.28: 7643 3.28 - 3.82: 12942 3.82 - 4.36: 15748 4.36 - 4.90: 28115 Nonbonded interactions: 65089 Sorted by model distance: nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.208 3.040 nonbonded pdb=" O TYR B 186 " pdb=" OH TYR B 192 " model vdw 2.210 3.040 nonbonded pdb=" OG SER D 92 " pdb=" OH TYR R 505 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 205 " pdb=" OE1 GLN A 206 " model vdw 2.266 3.040 nonbonded pdb=" OG SER A 35 " pdb=" OD2 ASP A 99 " model vdw 2.280 3.040 ... (remaining 65084 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 'D' and (resid 1 through 2 or resid 4 through 13 or resid 15 through 29 o \ r resid 32 through 84 or resid 86 through 91 or resid 95 or resid 97 through 100 \ or resid 102 through 104 or resid 107 through 108)) selection = (chain 'L' and (resid 1 through 2 or resid 4 through 13 or resid 15 through 29 o \ r resid 32 through 84 or resid 86 through 91 or resid 95 or resid 97 through 100 \ or resid 102 through 104 or resid 107 through 108)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.003 0.026 8627 Z= 0.127 Angle : 0.507 6.334 11745 Z= 0.267 Chirality : 0.041 0.280 1297 Planarity : 0.004 0.031 1498 Dihedral : 10.491 118.981 3117 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.65 % Allowed : 3.69 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.27), residues: 1076 helix: -2.72 (0.67), residues: 39 sheet: 0.69 (0.26), residues: 449 loop : -0.10 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 71 TYR 0.013 0.001 TYR C 33 PHE 0.010 0.001 PHE R 486 TRP 0.011 0.001 TRP H 110 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8611) covalent geometry : angle 0.50397 (11709) SS BOND : bond 0.00388 ( 12) SS BOND : angle 0.66265 ( 24) hydrogen bonds : bond 0.26985 ( 275) hydrogen bonds : angle 9.82787 ( 768) link_BETA1-4 : bond 0.00546 ( 2) link_BETA1-4 : angle 1.83766 ( 6) link_BETA1-6 : bond 0.00575 ( 1) link_BETA1-6 : angle 1.24036 ( 3) link_NAG-ASN : bond 0.00380 ( 1) link_NAG-ASN : angle 1.98180 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 227 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 127 SER cc_start: 0.8291 (t) cc_final: 0.7940 (p) REVERT: A 129 SER cc_start: 0.8298 (t) cc_final: 0.8031 (p) REVERT: B 27 GLN cc_start: 0.8177 (mt0) cc_final: 0.7920 (mt0) REVERT: B 73 THR cc_start: 0.8161 (m) cc_final: 0.7896 (t) REVERT: B 136 LEU cc_start: 0.8521 (mp) cc_final: 0.8302 (mp) REVERT: B 163 VAL cc_start: 0.8772 (t) cc_final: 0.8564 (p) REVERT: B 176 SER cc_start: 0.8274 (t) cc_final: 0.8058 (m) REVERT: C 66 ARG cc_start: 0.8616 (mtm110) cc_final: 0.8339 (mtp180) REVERT: C 69 ILE cc_start: 0.8477 (tt) cc_final: 0.8216 (tt) REVERT: H 84 SER cc_start: 0.8714 (m) cc_final: 0.8379 (t) REVERT: L 4 MET cc_start: 0.7157 (mmm) cc_final: 0.6296 (mmm) REVERT: L 104 LYS cc_start: 0.7921 (tttt) cc_final: 0.7716 (tttp) REVERT: R 335 LEU cc_start: 0.8117 (mp) cc_final: 0.7902 (mt) REVERT: R 357 ARG cc_start: 0.7013 (ttt90) cc_final: 0.6786 (ttt90) REVERT: R 438 SER cc_start: 0.8532 (p) cc_final: 0.8261 (p) outliers start: 6 outliers final: 1 residues processed: 230 average time/residue: 0.0911 time to fit residues: 28.8106 Evaluate side-chains 184 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.0370 chunk 61 optimal weight: 0.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN C 81 GLN D 37 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN R 440 ASN R 450 ASN R 506 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106564 restraints weight = 13009.338| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.28 r_work: 0.3279 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8627 Z= 0.177 Angle : 0.598 9.455 11745 Z= 0.309 Chirality : 0.044 0.163 1297 Planarity : 0.004 0.035 1498 Dihedral : 8.687 106.613 1273 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.74 % Allowed : 11.73 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.26), residues: 1076 helix: -2.93 (0.53), residues: 46 sheet: 0.73 (0.26), residues: 464 loop : -0.22 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 71 TYR 0.019 0.002 TYR C 105 PHE 0.019 0.002 PHE R 486 TRP 0.014 0.002 TRP H 110 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8611) covalent geometry : angle 0.59223 (11709) SS BOND : bond 0.00968 ( 12) SS BOND : angle 1.21958 ( 24) hydrogen bonds : bond 0.04897 ( 275) hydrogen bonds : angle 6.69684 ( 768) link_BETA1-4 : bond 0.00622 ( 2) link_BETA1-4 : angle 2.58429 ( 6) link_BETA1-6 : bond 0.01183 ( 1) link_BETA1-6 : angle 1.59071 ( 3) link_NAG-ASN : bond 0.00387 ( 1) link_NAG-ASN : angle 1.88389 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.312 Fit side-chains REVERT: A 127 SER cc_start: 0.8499 (t) cc_final: 0.8173 (p) REVERT: A 129 SER cc_start: 0.8599 (t) cc_final: 0.8320 (p) REVERT: B 27 GLN cc_start: 0.8462 (mt0) cc_final: 0.8210 (mt0) REVERT: B 118 PHE cc_start: 0.9082 (m-80) cc_final: 0.8649 (m-80) REVERT: B 163 VAL cc_start: 0.8907 (t) cc_final: 0.8525 (p) REVERT: C 66 ARG cc_start: 0.8773 (mtm110) cc_final: 0.8437 (mtp180) REVERT: D 71 PHE cc_start: 0.8114 (m-80) cc_final: 0.7822 (m-80) REVERT: H 84 SER cc_start: 0.8828 (m) cc_final: 0.8410 (t) REVERT: L 4 MET cc_start: 0.7673 (mmm) cc_final: 0.6786 (mmm) REVERT: L 104 LYS cc_start: 0.8431 (tttt) cc_final: 0.8226 (tttp) REVERT: R 357 ARG cc_start: 0.8118 (ttt90) cc_final: 0.7752 (ttt90) REVERT: R 394 ASN cc_start: 0.7624 (m-40) cc_final: 0.6828 (m-40) REVERT: R 439 ASN cc_start: 0.8349 (t0) cc_final: 0.7977 (t0) outliers start: 16 outliers final: 11 residues processed: 191 average time/residue: 0.0906 time to fit residues: 23.7392 Evaluate side-chains 184 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN B 166 GLN C 76 ASN ** D 90 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 = 0.3677 r_free = 0.3677 target = 0.125623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105932 restraints weight = 12816.959| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.27 r_work: 0.3273 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8627 Z= 0.172 Angle : 0.580 8.436 11745 Z= 0.298 Chirality : 0.044 0.156 1297 Planarity : 0.004 0.036 1498 Dihedral : 7.726 104.995 1273 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.61 % Allowed : 13.57 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.26), residues: 1076 helix: -2.83 (0.54), residues: 46 sheet: 0.65 (0.25), residues: 466 loop : -0.27 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.019 0.002 TYR C 105 PHE 0.015 0.002 PHE R 456 TRP 0.012 0.001 TRP H 110 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8611) covalent geometry : angle 0.57348 (11709) SS BOND : bond 0.00619 ( 12) SS BOND : angle 1.34070 ( 24) hydrogen bonds : bond 0.04446 ( 275) hydrogen bonds : angle 6.20847 ( 768) link_BETA1-4 : bond 0.00461 ( 2) link_BETA1-4 : angle 2.46266 ( 6) link_BETA1-6 : bond 0.00984 ( 1) link_BETA1-6 : angle 1.73159 ( 3) link_NAG-ASN : bond 0.00448 ( 1) link_NAG-ASN : angle 1.98972 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.249 Fit side-chains REVERT: A 127 SER cc_start: 0.8469 (t) cc_final: 0.8139 (p) REVERT: A 129 SER cc_start: 0.8629 (t) cc_final: 0.8344 (p) REVERT: A 157 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7335 (ttmm) REVERT: B 27 GLN cc_start: 0.8485 (mt0) cc_final: 0.8238 (mt0) REVERT: B 118 PHE cc_start: 0.9039 (m-80) cc_final: 0.8676 (m-80) REVERT: B 163 VAL cc_start: 0.8877 (t) cc_final: 0.8521 (p) REVERT: C 66 ARG cc_start: 0.8785 (mtm110) cc_final: 0.8457 (mtp180) REVERT: D 71 PHE cc_start: 0.8178 (m-80) cc_final: 0.7872 (m-80) REVERT: H 84 SER cc_start: 0.8849 (m) cc_final: 0.8449 (t) REVERT: L 4 MET cc_start: 0.7617 (mmm) cc_final: 0.6818 (mmm) REVERT: L 104 LYS cc_start: 0.8440 (tttt) cc_final: 0.8176 (tttp) REVERT: R 357 ARG cc_start: 0.8150 (ttt90) cc_final: 0.7762 (ttt90) REVERT: R 390 LEU cc_start: 0.8377 (mp) cc_final: 0.8118 (mm) REVERT: R 394 ASN cc_start: 0.7628 (m-40) cc_final: 0.6847 (m-40) REVERT: R 439 ASN cc_start: 0.8366 (t0) cc_final: 0.8009 (t0) outliers start: 24 outliers final: 18 residues processed: 188 average time/residue: 0.0893 time to fit residues: 23.3142 Evaluate side-chains 196 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 89 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN R 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106237 restraints weight = 13026.927| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.29 r_work: 0.3274 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8627 Z= 0.146 Angle : 0.556 7.481 11745 Z= 0.286 Chirality : 0.043 0.152 1297 Planarity : 0.004 0.033 1498 Dihedral : 7.179 101.109 1273 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.50 % Allowed : 13.46 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.26), residues: 1076 helix: -2.77 (0.55), residues: 46 sheet: 0.56 (0.25), residues: 472 loop : -0.24 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.018 0.001 TYR C 105 PHE 0.017 0.001 PHE R 392 TRP 0.010 0.001 TRP H 110 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8611) covalent geometry : angle 0.54990 (11709) SS BOND : bond 0.00537 ( 12) SS BOND : angle 1.23163 ( 24) hydrogen bonds : bond 0.03885 ( 275) hydrogen bonds : angle 5.94947 ( 768) link_BETA1-4 : bond 0.00531 ( 2) link_BETA1-4 : angle 2.26341 ( 6) link_BETA1-6 : bond 0.00836 ( 1) link_BETA1-6 : angle 1.72954 ( 3) link_NAG-ASN : bond 0.00454 ( 1) link_NAG-ASN : angle 1.90861 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.324 Fit side-chains REVERT: A 127 SER cc_start: 0.8424 (t) cc_final: 0.8092 (p) REVERT: A 129 SER cc_start: 0.8634 (t) cc_final: 0.8347 (p) REVERT: A 157 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7275 (ttmm) REVERT: B 27 GLN cc_start: 0.8443 (mt0) cc_final: 0.8209 (mt0) REVERT: B 118 PHE cc_start: 0.9033 (m-80) cc_final: 0.8713 (m-80) REVERT: D 71 PHE cc_start: 0.8164 (m-80) cc_final: 0.7830 (m-80) REVERT: H 84 SER cc_start: 0.8843 (m) cc_final: 0.8451 (t) REVERT: L 4 MET cc_start: 0.7588 (mmm) cc_final: 0.6714 (mmm) REVERT: L 104 LYS cc_start: 0.8447 (tttt) cc_final: 0.8174 (tttp) REVERT: R 357 ARG cc_start: 0.8138 (ttt90) cc_final: 0.7730 (ttt90) REVERT: R 390 LEU cc_start: 0.8340 (mp) cc_final: 0.8084 (mm) REVERT: R 394 ASN cc_start: 0.7641 (m-40) cc_final: 0.6823 (m-40) REVERT: R 406 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7771 (mt-10) REVERT: R 439 ASN cc_start: 0.8360 (t0) cc_final: 0.8021 (t0) outliers start: 23 outliers final: 16 residues processed: 186 average time/residue: 0.0972 time to fit residues: 24.8128 Evaluate side-chains 192 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 0.0570 chunk 76 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN C 76 ASN ** D 90 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 = 0.3677 r_free = 0.3677 target = 0.125857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106232 restraints weight = 12943.908| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.28 r_work: 0.3273 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8627 Z= 0.150 Angle : 0.547 7.397 11745 Z= 0.282 Chirality : 0.043 0.150 1297 Planarity : 0.004 0.035 1498 Dihedral : 6.956 100.630 1273 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.82 % Allowed : 14.01 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.26), residues: 1076 helix: -2.70 (0.57), residues: 46 sheet: 0.56 (0.25), residues: 473 loop : -0.22 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.019 0.001 TYR H 79 PHE 0.014 0.001 PHE R 392 TRP 0.011 0.001 TRP H 110 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8611) covalent geometry : angle 0.54137 (11709) SS BOND : bond 0.00552 ( 12) SS BOND : angle 1.24459 ( 24) hydrogen bonds : bond 0.03755 ( 275) hydrogen bonds : angle 5.79557 ( 768) link_BETA1-4 : bond 0.00442 ( 2) link_BETA1-4 : angle 2.00636 ( 6) link_BETA1-6 : bond 0.01149 ( 1) link_BETA1-6 : angle 1.92545 ( 3) link_NAG-ASN : bond 0.00433 ( 1) link_NAG-ASN : angle 1.96886 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.381 Fit side-chains REVERT: A 127 SER cc_start: 0.8414 (t) cc_final: 0.8087 (p) REVERT: A 129 SER cc_start: 0.8633 (t) cc_final: 0.8341 (p) REVERT: A 157 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7282 (ttmm) REVERT: B 27 GLN cc_start: 0.8458 (mt0) cc_final: 0.8235 (mt0) REVERT: B 118 PHE cc_start: 0.9026 (m-80) cc_final: 0.8717 (m-80) REVERT: B 163 VAL cc_start: 0.8863 (t) cc_final: 0.8519 (p) REVERT: B 183 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7229 (ttmt) REVERT: H 84 SER cc_start: 0.8830 (m) cc_final: 0.8451 (t) REVERT: L 4 MET cc_start: 0.7579 (mmm) cc_final: 0.6749 (mmm) REVERT: L 104 LYS cc_start: 0.8480 (tttt) cc_final: 0.8181 (tttp) REVERT: R 354 ASN cc_start: 0.8552 (t0) cc_final: 0.8246 (t0) REVERT: R 357 ARG cc_start: 0.8140 (ttt90) cc_final: 0.7697 (ttt90) REVERT: R 394 ASN cc_start: 0.7608 (m-40) cc_final: 0.6796 (m-40) REVERT: R 406 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7774 (mt-10) REVERT: R 439 ASN cc_start: 0.8344 (t0) cc_final: 0.8014 (t0) REVERT: R 494 SER cc_start: 0.8535 (m) cc_final: 0.8316 (p) outliers start: 26 outliers final: 18 residues processed: 184 average time/residue: 0.0940 time to fit residues: 23.8423 Evaluate side-chains 194 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 103 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN D 34 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106407 restraints weight = 12847.720| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.27 r_work: 0.3271 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8627 Z= 0.170 Angle : 0.584 13.213 11745 Z= 0.299 Chirality : 0.044 0.238 1297 Planarity : 0.004 0.036 1498 Dihedral : 6.840 100.742 1272 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.50 % Allowed : 14.66 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.26), residues: 1076 helix: -2.72 (0.57), residues: 46 sheet: 0.53 (0.25), residues: 475 loop : -0.21 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.020 0.002 TYR C 105 PHE 0.014 0.001 PHE R 456 TRP 0.011 0.001 TRP H 110 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8611) covalent geometry : angle 0.56920 (11709) SS BOND : bond 0.01095 ( 12) SS BOND : angle 2.63864 ( 24) hydrogen bonds : bond 0.03753 ( 275) hydrogen bonds : angle 5.77130 ( 768) link_BETA1-4 : bond 0.00400 ( 2) link_BETA1-4 : angle 1.93715 ( 6) link_BETA1-6 : bond 0.01076 ( 1) link_BETA1-6 : angle 1.97054 ( 3) link_NAG-ASN : bond 0.00412 ( 1) link_NAG-ASN : angle 2.05243 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.383 Fit side-chains REVERT: A 127 SER cc_start: 0.8410 (t) cc_final: 0.8079 (p) REVERT: A 129 SER cc_start: 0.8651 (t) cc_final: 0.8357 (p) REVERT: A 157 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7288 (ttmm) REVERT: B 27 GLN cc_start: 0.8446 (mt0) cc_final: 0.8237 (mt0) REVERT: B 118 PHE cc_start: 0.9018 (m-80) cc_final: 0.8698 (m-80) REVERT: B 163 VAL cc_start: 0.8871 (t) cc_final: 0.8532 (p) REVERT: H 84 SER cc_start: 0.8839 (m) cc_final: 0.8470 (t) REVERT: L 4 MET cc_start: 0.7586 (mmm) cc_final: 0.6752 (mmm) REVERT: L 104 LYS cc_start: 0.8496 (tttt) cc_final: 0.8200 (tttp) REVERT: R 354 ASN cc_start: 0.8555 (t0) cc_final: 0.8255 (t0) REVERT: R 357 ARG cc_start: 0.8151 (ttt90) cc_final: 0.7711 (ttt90) REVERT: R 394 ASN cc_start: 0.7618 (m-40) cc_final: 0.6791 (m-40) REVERT: R 406 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7777 (mt-10) REVERT: R 439 ASN cc_start: 0.8343 (t0) cc_final: 0.8011 (t0) outliers start: 23 outliers final: 18 residues processed: 182 average time/residue: 0.0901 time to fit residues: 22.5825 Evaluate side-chains 185 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 104 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN C 76 ASN ** D 90 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 = 0.3657 r_free = 0.3657 target = 0.124338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104714 restraints weight = 12933.321| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.27 r_work: 0.3243 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 8627 Z= 0.234 Angle : 0.622 10.565 11745 Z= 0.322 Chirality : 0.045 0.181 1297 Planarity : 0.004 0.042 1498 Dihedral : 7.212 105.080 1272 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.71 % Allowed : 14.66 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.26), residues: 1076 helix: -2.81 (0.56), residues: 46 sheet: 0.45 (0.25), residues: 475 loop : -0.34 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.022 0.002 TYR C 105 PHE 0.017 0.002 PHE R 456 TRP 0.013 0.002 TRP H 110 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 8611) covalent geometry : angle 0.61217 (11709) SS BOND : bond 0.00979 ( 12) SS BOND : angle 2.09504 ( 24) hydrogen bonds : bond 0.04268 ( 275) hydrogen bonds : angle 5.95243 ( 768) link_BETA1-4 : bond 0.00398 ( 2) link_BETA1-4 : angle 2.05502 ( 6) link_BETA1-6 : bond 0.01023 ( 1) link_BETA1-6 : angle 1.80444 ( 3) link_NAG-ASN : bond 0.00424 ( 1) link_NAG-ASN : angle 2.47113 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.239 Fit side-chains REVERT: A 81 MET cc_start: 0.8017 (ttp) cc_final: 0.7719 (ttp) REVERT: A 127 SER cc_start: 0.8325 (t) cc_final: 0.8045 (p) REVERT: A 129 SER cc_start: 0.8642 (t) cc_final: 0.8350 (p) REVERT: B 27 GLN cc_start: 0.8525 (mt0) cc_final: 0.8322 (mt0) REVERT: B 118 PHE cc_start: 0.9000 (m-80) cc_final: 0.8683 (m-80) REVERT: B 163 VAL cc_start: 0.8842 (t) cc_final: 0.8529 (p) REVERT: B 183 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7345 (ttmt) REVERT: C 49 SER cc_start: 0.8722 (t) cc_final: 0.8469 (p) REVERT: D 7 SER cc_start: 0.8132 (t) cc_final: 0.7908 (t) REVERT: H 84 SER cc_start: 0.8829 (m) cc_final: 0.8470 (t) REVERT: L 104 LYS cc_start: 0.8499 (tttt) cc_final: 0.8197 (tttp) REVERT: R 354 ASN cc_start: 0.8594 (t0) cc_final: 0.8259 (t0) REVERT: R 357 ARG cc_start: 0.8180 (ttt90) cc_final: 0.7751 (ttt90) REVERT: R 390 LEU cc_start: 0.8542 (mp) cc_final: 0.8263 (mm) REVERT: R 394 ASN cc_start: 0.7711 (m-40) cc_final: 0.6876 (m-40) REVERT: R 439 ASN cc_start: 0.8275 (t0) cc_final: 0.7956 (t0) outliers start: 25 outliers final: 19 residues processed: 185 average time/residue: 0.0926 time to fit residues: 23.5531 Evaluate side-chains 193 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN C 76 ASN ** D 90 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 = 0.3663 r_free = 0.3663 target = 0.124891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105585 restraints weight = 12792.668| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.15 r_work: 0.3263 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8627 Z= 0.205 Angle : 0.605 9.351 11745 Z= 0.311 Chirality : 0.044 0.159 1297 Planarity : 0.004 0.043 1498 Dihedral : 7.075 102.697 1272 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.50 % Allowed : 14.98 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.26), residues: 1076 helix: -2.79 (0.57), residues: 46 sheet: 0.41 (0.25), residues: 478 loop : -0.37 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.022 0.002 TYR C 105 PHE 0.016 0.002 PHE R 456 TRP 0.012 0.002 TRP H 110 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 8611) covalent geometry : angle 0.59327 (11709) SS BOND : bond 0.00865 ( 12) SS BOND : angle 2.32706 ( 24) hydrogen bonds : bond 0.04027 ( 275) hydrogen bonds : angle 5.87023 ( 768) link_BETA1-4 : bond 0.00423 ( 2) link_BETA1-4 : angle 1.89260 ( 6) link_BETA1-6 : bond 0.01096 ( 1) link_BETA1-6 : angle 1.93922 ( 3) link_NAG-ASN : bond 0.00356 ( 1) link_NAG-ASN : angle 2.25725 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.323 Fit side-chains REVERT: A 81 MET cc_start: 0.7977 (ttp) cc_final: 0.7631 (ttp) REVERT: A 127 SER cc_start: 0.8311 (t) cc_final: 0.8037 (p) REVERT: A 129 SER cc_start: 0.8649 (t) cc_final: 0.8360 (p) REVERT: A 157 LYS cc_start: 0.7669 (ttmm) cc_final: 0.7292 (ttmm) REVERT: B 118 PHE cc_start: 0.8984 (m-80) cc_final: 0.8666 (m-80) REVERT: B 163 VAL cc_start: 0.8853 (t) cc_final: 0.8592 (p) REVERT: B 183 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7320 (ttmt) REVERT: C 49 SER cc_start: 0.8689 (t) cc_final: 0.8423 (p) REVERT: D 7 SER cc_start: 0.8071 (t) cc_final: 0.7838 (t) REVERT: H 84 SER cc_start: 0.8829 (m) cc_final: 0.8483 (t) REVERT: L 4 MET cc_start: 0.7805 (mmm) cc_final: 0.6907 (mmm) REVERT: L 104 LYS cc_start: 0.8473 (tttt) cc_final: 0.8172 (tttp) REVERT: R 354 ASN cc_start: 0.8527 (t0) cc_final: 0.8183 (t0) REVERT: R 357 ARG cc_start: 0.8132 (ttt90) cc_final: 0.7692 (ttt90) REVERT: R 394 ASN cc_start: 0.7643 (m-40) cc_final: 0.6826 (m-40) REVERT: R 439 ASN cc_start: 0.8309 (t0) cc_final: 0.7990 (t0) outliers start: 23 outliers final: 20 residues processed: 177 average time/residue: 0.0840 time to fit residues: 20.7952 Evaluate side-chains 188 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 103 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 102 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN D 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106999 restraints weight = 12832.755| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.17 r_work: 0.3283 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8627 Z= 0.125 Angle : 0.549 8.631 11745 Z= 0.281 Chirality : 0.043 0.151 1297 Planarity : 0.004 0.040 1498 Dihedral : 6.779 99.047 1272 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.85 % Allowed : 15.74 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.26), residues: 1076 helix: -2.50 (0.66), residues: 39 sheet: 0.51 (0.25), residues: 475 loop : -0.37 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 71 TYR 0.018 0.001 TYR C 105 PHE 0.012 0.001 PHE R 456 TRP 0.011 0.001 TRP R 353 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8611) covalent geometry : angle 0.54052 (11709) SS BOND : bond 0.00665 ( 12) SS BOND : angle 1.84097 ( 24) hydrogen bonds : bond 0.03394 ( 275) hydrogen bonds : angle 5.64426 ( 768) link_BETA1-4 : bond 0.00459 ( 2) link_BETA1-4 : angle 1.75456 ( 6) link_BETA1-6 : bond 0.01183 ( 1) link_BETA1-6 : angle 1.97052 ( 3) link_NAG-ASN : bond 0.00370 ( 1) link_NAG-ASN : angle 1.84753 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.335 Fit side-chains REVERT: A 127 SER cc_start: 0.8316 (t) cc_final: 0.8048 (p) REVERT: A 129 SER cc_start: 0.8640 (t) cc_final: 0.8352 (p) REVERT: B 163 VAL cc_start: 0.8829 (t) cc_final: 0.8535 (p) REVERT: C 66 ARG cc_start: 0.8767 (mtm110) cc_final: 0.8479 (mtp180) REVERT: H 84 SER cc_start: 0.8826 (m) cc_final: 0.8481 (t) REVERT: L 4 MET cc_start: 0.7726 (mmm) cc_final: 0.7081 (mtp) REVERT: L 104 LYS cc_start: 0.8458 (tttt) cc_final: 0.8166 (tttp) REVERT: R 354 ASN cc_start: 0.8439 (t0) cc_final: 0.8103 (t0) REVERT: R 357 ARG cc_start: 0.8108 (ttt90) cc_final: 0.7649 (ttt90) REVERT: R 394 ASN cc_start: 0.7559 (m-40) cc_final: 0.6706 (m-40) REVERT: R 439 ASN cc_start: 0.8292 (t0) cc_final: 0.7972 (t0) outliers start: 17 outliers final: 14 residues processed: 177 average time/residue: 0.0904 time to fit residues: 22.2289 Evaluate side-chains 180 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN D 6 GLN D 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.104142 restraints weight = 12850.404| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.27 r_work: 0.3243 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8627 Z= 0.258 Angle : 0.623 8.677 11745 Z= 0.322 Chirality : 0.046 0.150 1297 Planarity : 0.005 0.043 1498 Dihedral : 7.133 103.813 1272 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.74 % Allowed : 16.18 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.26), residues: 1076 helix: -2.78 (0.56), residues: 46 sheet: 0.36 (0.25), residues: 482 loop : -0.35 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 71 TYR 0.022 0.002 TYR L 32 PHE 0.020 0.002 PHE R 456 TRP 0.013 0.002 TRP H 110 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 8611) covalent geometry : angle 0.61170 (11709) SS BOND : bond 0.00874 ( 12) SS BOND : angle 2.26463 ( 24) hydrogen bonds : bond 0.04223 ( 275) hydrogen bonds : angle 5.83640 ( 768) link_BETA1-4 : bond 0.00435 ( 2) link_BETA1-4 : angle 2.08266 ( 6) link_BETA1-6 : bond 0.00848 ( 1) link_BETA1-6 : angle 1.92329 ( 3) link_NAG-ASN : bond 0.00368 ( 1) link_NAG-ASN : angle 2.36630 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.373 Fit side-chains REVERT: A 81 MET cc_start: 0.8023 (ttp) cc_final: 0.7667 (ttp) REVERT: A 127 SER cc_start: 0.8333 (t) cc_final: 0.8070 (p) REVERT: A 157 LYS cc_start: 0.7709 (ttmm) cc_final: 0.7343 (ttmm) REVERT: B 163 VAL cc_start: 0.8846 (t) cc_final: 0.8568 (p) REVERT: C 49 SER cc_start: 0.8717 (t) cc_final: 0.8474 (p) REVERT: D 7 SER cc_start: 0.8124 (t) cc_final: 0.7890 (t) REVERT: H 84 SER cc_start: 0.8844 (m) cc_final: 0.8523 (t) REVERT: L 4 MET cc_start: 0.7792 (mmm) cc_final: 0.7057 (mtp) REVERT: L 104 LYS cc_start: 0.8482 (tttt) cc_final: 0.8188 (tttp) REVERT: R 354 ASN cc_start: 0.8560 (t0) cc_final: 0.8215 (t0) REVERT: R 357 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7687 (ttt90) REVERT: R 394 ASN cc_start: 0.7644 (m-40) cc_final: 0.6792 (m-40) REVERT: R 439 ASN cc_start: 0.8312 (t0) cc_final: 0.7985 (t0) outliers start: 16 outliers final: 16 residues processed: 172 average time/residue: 0.0902 time to fit residues: 21.6877 Evaluate side-chains 179 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 93 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 86 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 88 optimal weight: 0.3980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN D 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.125909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106211 restraints weight = 12754.211| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.28 r_work: 0.3270 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8627 Z= 0.123 Angle : 0.562 8.959 11745 Z= 0.286 Chirality : 0.043 0.151 1297 Planarity : 0.004 0.045 1498 Dihedral : 6.849 99.929 1272 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.63 % Allowed : 16.50 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.26), residues: 1076 helix: -2.69 (0.57), residues: 46 sheet: 0.43 (0.25), residues: 475 loop : -0.32 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.018 0.001 TYR H 79 PHE 0.019 0.001 PHE B 118 TRP 0.011 0.001 TRP R 353 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8611) covalent geometry : angle 0.55433 (11709) SS BOND : bond 0.00647 ( 12) SS BOND : angle 1.73229 ( 24) hydrogen bonds : bond 0.03452 ( 275) hydrogen bonds : angle 5.65558 ( 768) link_BETA1-4 : bond 0.00476 ( 2) link_BETA1-4 : angle 1.75371 ( 6) link_BETA1-6 : bond 0.01077 ( 1) link_BETA1-6 : angle 1.92441 ( 3) link_NAG-ASN : bond 0.00358 ( 1) link_NAG-ASN : angle 2.01780 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2452.26 seconds wall clock time: 42 minutes 39.12 seconds (2559.12 seconds total)