Starting phenix.real_space_refine on Sun May 11 20:47:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpy_37726/05_2025/8wpy_37726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpy_37726/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wpy_37726/05_2025/8wpy_37726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpy_37726/05_2025/8wpy_37726.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpy_37726/05_2025/8wpy_37726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpy_37726/05_2025/8wpy_37726.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.62, per 1000 atoms: 0.67 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.44 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: 2.68 Time building geometry restraints manager: 2.80 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: 2.490 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.590 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.730 ------------------------------------------------------------------------------- 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 : 3.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (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 TRP 0.011 0.001 TRP H 110 HIS 0.003 0.001 HIS B 92 PHE 0.010 0.001 PHE R 486 TYR 0.013 0.001 TYR C 33 ARG 0.002 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 1) link_NAG-ASN : angle 1.98180 ( 3) link_BETA1-4 : bond 0.00546 ( 2) link_BETA1-4 : angle 1.83766 ( 6) hydrogen bonds : bond 0.26985 ( 275) hydrogen bonds : angle 9.82787 ( 768) link_BETA1-6 : bond 0.00575 ( 1) link_BETA1-6 : angle 1.24036 ( 3) SS BOND : bond 0.00388 ( 12) SS BOND : angle 0.66265 ( 24) covalent geometry : bond 0.00256 ( 8611) covalent geometry : angle 0.50397 (11709) *********************** 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 : 0.901 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: 0.2028 time to fit residues: 63.1626 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 : 0.914 ------------------------------------------------------------------------------- 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 88 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 = 0.3685 r_free = 0.3685 target = 0.126145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106387 restraints weight = 12729.239| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.25 r_work: 0.3275 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8627 Z= 0.183 Angle : 0.595 8.927 11745 Z= 0.309 Chirality : 0.044 0.162 1297 Planarity : 0.004 0.036 1498 Dihedral : 8.785 107.261 1273 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1076 helix: -2.91 (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 TRP 0.014 0.002 TRP H 110 HIS 0.004 0.001 HIS B 92 PHE 0.018 0.002 PHE R 486 TYR 0.018 0.002 TYR C 105 ARG 0.004 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 1) link_NAG-ASN : angle 1.85939 ( 3) link_BETA1-4 : bond 0.00366 ( 2) link_BETA1-4 : angle 2.55604 ( 6) hydrogen bonds : bond 0.05480 ( 275) hydrogen bonds : angle 6.78965 ( 768) link_BETA1-6 : bond 0.01007 ( 1) link_BETA1-6 : angle 1.53575 ( 3) SS BOND : bond 0.00711 ( 12) SS BOND : angle 1.26217 ( 24) covalent geometry : bond 0.00417 ( 8611) covalent geometry : angle 0.58931 (11709) *********************** 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 205 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.907 Fit side-chains REVERT: A 127 SER cc_start: 0.8501 (t) cc_final: 0.8175 (p) REVERT: A 129 SER cc_start: 0.8603 (t) cc_final: 0.8323 (p) REVERT: B 27 GLN cc_start: 0.8463 (mt0) cc_final: 0.8210 (mt0) REVERT: B 118 PHE cc_start: 0.9085 (m-80) cc_final: 0.8647 (m-80) REVERT: B 163 VAL cc_start: 0.8923 (t) cc_final: 0.8545 (p) REVERT: B 183 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7039 (ttmt) REVERT: C 66 ARG cc_start: 0.8768 (mtm110) cc_final: 0.8432 (mtp180) REVERT: D 71 PHE cc_start: 0.8118 (m-80) cc_final: 0.7840 (m-80) REVERT: H 84 SER cc_start: 0.8825 (m) cc_final: 0.8405 (t) REVERT: L 4 MET cc_start: 0.7668 (mmm) cc_final: 0.6784 (mmm) REVERT: L 104 LYS cc_start: 0.8427 (tttt) cc_final: 0.8215 (tttp) REVERT: R 357 ARG cc_start: 0.8119 (ttt90) cc_final: 0.7721 (ttt90) REVERT: R 394 ASN cc_start: 0.7625 (m-40) cc_final: 0.6822 (m-40) REVERT: R 439 ASN cc_start: 0.8330 (t0) cc_final: 0.7963 (t0) outliers start: 16 outliers final: 12 residues processed: 193 average time/residue: 0.2081 time to fit residues: 54.4800 Evaluate side-chains 188 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 183 LYS 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 7 SER 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 9 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** H 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105555 restraints weight = 13019.324| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.29 r_work: 0.3265 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8627 Z= 0.188 Angle : 0.592 8.322 11745 Z= 0.305 Chirality : 0.044 0.155 1297 Planarity : 0.004 0.037 1498 Dihedral : 7.836 105.941 1273 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.15 % Allowed : 12.70 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1076 helix: -2.89 (0.53), residues: 46 sheet: 0.64 (0.25), residues: 466 loop : -0.31 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 110 HIS 0.004 0.001 HIS B 92 PHE 0.016 0.002 PHE R 456 TYR 0.019 0.002 TYR H 79 ARG 0.004 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 1) link_NAG-ASN : angle 2.01413 ( 3) link_BETA1-4 : bond 0.00464 ( 2) link_BETA1-4 : angle 2.47873 ( 6) hydrogen bonds : bond 0.04578 ( 275) hydrogen bonds : angle 6.24980 ( 768) link_BETA1-6 : bond 0.00882 ( 1) link_BETA1-6 : angle 1.64807 ( 3) SS BOND : bond 0.00658 ( 12) SS BOND : angle 1.30219 ( 24) covalent geometry : bond 0.00439 ( 8611) covalent geometry : angle 0.58588 (11709) *********************** 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 207 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.926 Fit side-chains REVERT: A 115 ASP cc_start: 0.8315 (p0) cc_final: 0.8087 (p0) REVERT: A 127 SER cc_start: 0.8467 (t) cc_final: 0.8137 (p) REVERT: A 129 SER cc_start: 0.8604 (t) cc_final: 0.8316 (p) REVERT: A 157 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7327 (ttmm) REVERT: B 27 GLN cc_start: 0.8494 (mt0) cc_final: 0.8258 (mt0) REVERT: B 118 PHE cc_start: 0.9038 (m-80) cc_final: 0.8669 (m-80) REVERT: B 163 VAL cc_start: 0.8883 (t) cc_final: 0.8535 (p) REVERT: C 66 ARG cc_start: 0.8791 (mtm110) cc_final: 0.8464 (mtp180) REVERT: D 71 PHE cc_start: 0.8191 (m-80) cc_final: 0.7897 (m-80) REVERT: H 84 SER cc_start: 0.8849 (m) cc_final: 0.8442 (t) REVERT: L 4 MET cc_start: 0.7619 (mmm) cc_final: 0.6814 (mmm) REVERT: L 104 LYS cc_start: 0.8449 (tttt) cc_final: 0.8178 (tttp) REVERT: R 357 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7773 (ttt90) REVERT: R 390 LEU cc_start: 0.8389 (mp) cc_final: 0.8128 (mm) REVERT: R 394 ASN cc_start: 0.7646 (m-40) cc_final: 0.6863 (m-40) REVERT: R 406 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7777 (mt-10) REVERT: R 439 ASN cc_start: 0.8352 (t0) cc_final: 0.7999 (t0) outliers start: 29 outliers final: 20 residues processed: 190 average time/residue: 0.2093 time to fit residues: 54.0784 Evaluate side-chains 199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 25 SER 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 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 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 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** R 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105271 restraints weight = 12918.946| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.28 r_work: 0.3262 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8627 Z= 0.179 Angle : 0.576 7.348 11745 Z= 0.297 Chirality : 0.044 0.149 1297 Planarity : 0.004 0.037 1498 Dihedral : 7.370 104.155 1273 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.61 % Allowed : 13.14 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1076 helix: -2.83 (0.54), residues: 46 sheet: 0.57 (0.25), residues: 461 loop : -0.31 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.003 0.001 HIS B 92 PHE 0.018 0.002 PHE R 392 TYR 0.019 0.002 TYR C 105 ARG 0.003 0.000 ARG R 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 1) link_NAG-ASN : angle 2.05951 ( 3) link_BETA1-4 : bond 0.00499 ( 2) link_BETA1-4 : angle 2.28356 ( 6) hydrogen bonds : bond 0.04125 ( 275) hydrogen bonds : angle 6.04319 ( 768) link_BETA1-6 : bond 0.01068 ( 1) link_BETA1-6 : angle 1.83822 ( 3) SS BOND : bond 0.00619 ( 12) SS BOND : angle 1.34348 ( 24) covalent geometry : bond 0.00417 ( 8611) covalent geometry : angle 0.56935 (11709) *********************** 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 199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.834 Fit side-chains REVERT: A 115 ASP cc_start: 0.8300 (p0) cc_final: 0.8077 (p0) REVERT: A 127 SER cc_start: 0.8417 (t) cc_final: 0.8083 (p) REVERT: A 129 SER cc_start: 0.8613 (t) cc_final: 0.8322 (p) REVERT: A 157 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7265 (ttmm) REVERT: B 6 GLN cc_start: 0.8515 (mt0) cc_final: 0.8300 (mt0) REVERT: B 27 GLN cc_start: 0.8467 (mt0) cc_final: 0.8241 (mt0) REVERT: B 118 PHE cc_start: 0.9044 (m-80) cc_final: 0.8721 (m-80) REVERT: B 163 VAL cc_start: 0.8898 (t) cc_final: 0.8562 (p) REVERT: H 84 SER cc_start: 0.8835 (m) cc_final: 0.8448 (t) REVERT: L 4 MET cc_start: 0.7588 (mmm) cc_final: 0.6767 (mmm) REVERT: L 104 LYS cc_start: 0.8445 (tttt) cc_final: 0.8174 (tttp) REVERT: R 357 ARG cc_start: 0.8138 (ttt90) cc_final: 0.7742 (ttt90) REVERT: R 390 LEU cc_start: 0.8384 (mp) cc_final: 0.8140 (mm) REVERT: R 394 ASN cc_start: 0.7657 (m-40) cc_final: 0.6862 (m-40) REVERT: R 406 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7790 (mt-10) REVERT: R 439 ASN cc_start: 0.8320 (t0) cc_final: 0.7986 (t0) outliers start: 24 outliers final: 17 residues processed: 182 average time/residue: 0.2119 time to fit residues: 52.6611 Evaluate side-chains 192 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 7 SER 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 44 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 104 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 ** 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 = 0.3648 r_free = 0.3648 target = 0.123737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.104181 restraints weight = 12805.499| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.25 r_work: 0.3238 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8627 Z= 0.273 Angle : 0.636 7.676 11745 Z= 0.332 Chirality : 0.046 0.155 1297 Planarity : 0.005 0.041 1498 Dihedral : 7.494 105.972 1273 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1076 helix: -2.96 (0.54), residues: 46 sheet: 0.48 (0.25), residues: 462 loop : -0.41 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 110 HIS 0.004 0.001 HIS B 92 PHE 0.019 0.002 PHE R 456 TYR 0.024 0.002 TYR L 32 ARG 0.004 0.001 ARG R 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 1) link_NAG-ASN : angle 2.54816 ( 3) link_BETA1-4 : bond 0.00428 ( 2) link_BETA1-4 : angle 2.25515 ( 6) hydrogen bonds : bond 0.04659 ( 275) hydrogen bonds : angle 6.18302 ( 768) link_BETA1-6 : bond 0.00848 ( 1) link_BETA1-6 : angle 1.79114 ( 3) SS BOND : bond 0.00856 ( 12) SS BOND : angle 1.66689 ( 24) covalent geometry : bond 0.00645 ( 8611) covalent geometry : angle 0.62814 (11709) *********************** 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 205 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.859 Fit side-chains REVERT: A 115 ASP cc_start: 0.8286 (p0) cc_final: 0.8082 (p0) REVERT: A 127 SER cc_start: 0.8391 (t) cc_final: 0.8045 (p) REVERT: A 129 SER cc_start: 0.8659 (t) cc_final: 0.8375 (p) REVERT: B 6 GLN cc_start: 0.8585 (mt0) cc_final: 0.8377 (mt0) REVERT: B 118 PHE cc_start: 0.9042 (m-80) cc_final: 0.8737 (m-80) REVERT: B 163 VAL cc_start: 0.8877 (t) cc_final: 0.8591 (p) REVERT: B 183 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7284 (ttmt) REVERT: C 4 LEU cc_start: 0.8660 (mt) cc_final: 0.8455 (mt) REVERT: C 49 SER cc_start: 0.8733 (t) cc_final: 0.8495 (p) REVERT: D 7 SER cc_start: 0.8164 (t) cc_final: 0.7933 (t) REVERT: H 84 SER cc_start: 0.8824 (m) cc_final: 0.8457 (t) REVERT: L 4 MET cc_start: 0.7632 (mmm) cc_final: 0.7051 (mtm) REVERT: L 104 LYS cc_start: 0.8513 (tttt) cc_final: 0.8206 (tttp) REVERT: R 354 ASN cc_start: 0.8607 (t0) cc_final: 0.8271 (t0) REVERT: R 357 ARG cc_start: 0.8171 (ttt90) cc_final: 0.7849 (ttt90) REVERT: R 439 ASN cc_start: 0.8257 (t0) cc_final: 0.7952 (t0) REVERT: R 494 SER cc_start: 0.8559 (m) cc_final: 0.8354 (p) outliers start: 26 outliers final: 21 residues processed: 190 average time/residue: 0.2027 time to fit residues: 53.1107 Evaluate side-chains 192 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 25 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 A residue 210 CYS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 132 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 108 LYS Chi-restraints excluded: chain H residue 7 SER 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 63 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.0270 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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** C 76 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 360 ASN R 440 ASN R 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.125990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106710 restraints weight = 12811.219| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.17 r_work: 0.3280 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8627 Z= 0.144 Angle : 0.575 12.585 11745 Z= 0.295 Chirality : 0.043 0.204 1297 Planarity : 0.004 0.038 1498 Dihedral : 7.117 101.216 1273 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.06 % Allowed : 15.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1076 helix: -2.83 (0.55), residues: 46 sheet: 0.51 (0.25), residues: 463 loop : -0.37 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 110 HIS 0.002 0.001 HIS A 214 PHE 0.015 0.001 PHE R 392 TYR 0.019 0.001 TYR C 105 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 1) link_NAG-ASN : angle 1.97087 ( 3) link_BETA1-4 : bond 0.00533 ( 2) link_BETA1-4 : angle 1.84329 ( 6) hydrogen bonds : bond 0.03670 ( 275) hydrogen bonds : angle 5.86061 ( 768) link_BETA1-6 : bond 0.00951 ( 1) link_BETA1-6 : angle 1.82793 ( 3) SS BOND : bond 0.01089 ( 12) SS BOND : angle 2.23949 ( 24) covalent geometry : bond 0.00334 ( 8611) covalent geometry : angle 0.56387 (11709) *********************** 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 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.852 Fit side-chains REVERT: A 127 SER cc_start: 0.8335 (t) cc_final: 0.7997 (p) REVERT: A 129 SER cc_start: 0.8627 (t) cc_final: 0.8343 (p) REVERT: A 157 LYS cc_start: 0.7623 (ttmm) cc_final: 0.7269 (ttmm) REVERT: B 118 PHE cc_start: 0.8997 (m-80) cc_final: 0.8690 (m-80) REVERT: B 163 VAL cc_start: 0.8807 (t) cc_final: 0.8464 (p) REVERT: H 84 SER cc_start: 0.8831 (m) cc_final: 0.8474 (t) REVERT: L 4 MET cc_start: 0.7561 (mmm) cc_final: 0.6744 (mmm) REVERT: L 104 LYS cc_start: 0.8478 (tttt) cc_final: 0.8175 (tttp) REVERT: R 354 ASN cc_start: 0.8496 (t0) cc_final: 0.8161 (t0) REVERT: R 357 ARG cc_start: 0.8098 (ttt90) cc_final: 0.7781 (ttt90) REVERT: R 439 ASN cc_start: 0.8256 (t0) cc_final: 0.7945 (t0) outliers start: 19 outliers final: 14 residues processed: 179 average time/residue: 0.2031 time to fit residues: 49.8206 Evaluate side-chains 178 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR 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 132 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 9 SER 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 1 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 34 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 = 0.3651 r_free = 0.3651 target = 0.123970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104352 restraints weight = 12851.122| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.27 r_work: 0.3240 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 8627 Z= 0.266 Angle : 0.638 11.211 11745 Z= 0.330 Chirality : 0.046 0.189 1297 Planarity : 0.005 0.042 1498 Dihedral : 7.236 104.606 1272 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.93 % Allowed : 15.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1076 helix: -2.94 (0.55), residues: 46 sheet: 0.41 (0.25), residues: 475 loop : -0.43 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 110 HIS 0.005 0.001 HIS B 92 PHE 0.019 0.002 PHE R 456 TYR 0.023 0.002 TYR L 32 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 1) link_NAG-ASN : angle 2.36799 ( 3) link_BETA1-4 : bond 0.00484 ( 2) link_BETA1-4 : angle 2.11089 ( 6) hydrogen bonds : bond 0.04365 ( 275) hydrogen bonds : angle 5.99797 ( 768) link_BETA1-6 : bond 0.00850 ( 1) link_BETA1-6 : angle 1.72657 ( 3) SS BOND : bond 0.01023 ( 12) SS BOND : angle 2.22114 ( 24) covalent geometry : bond 0.00628 ( 8611) covalent geometry : angle 0.62780 (11709) *********************** 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 199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.847 Fit side-chains REVERT: A 115 ASP cc_start: 0.8303 (p0) cc_final: 0.8081 (p0) REVERT: A 127 SER cc_start: 0.8323 (t) cc_final: 0.8039 (p) REVERT: A 129 SER cc_start: 0.8665 (t) cc_final: 0.8384 (p) REVERT: A 157 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7364 (ttmm) REVERT: B 163 VAL cc_start: 0.8828 (t) cc_final: 0.8514 (p) REVERT: B 183 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7324 (ttmt) REVERT: C 49 SER cc_start: 0.8742 (t) cc_final: 0.8486 (p) REVERT: D 7 SER cc_start: 0.8105 (t) cc_final: 0.7898 (t) REVERT: H 84 SER cc_start: 0.8838 (m) cc_final: 0.8484 (t) REVERT: L 4 MET cc_start: 0.7607 (mmm) cc_final: 0.6783 (mmm) REVERT: L 104 LYS cc_start: 0.8504 (tttt) cc_final: 0.8199 (tttp) REVERT: R 354 ASN cc_start: 0.8594 (t0) cc_final: 0.8255 (t0) REVERT: R 357 ARG cc_start: 0.8188 (ttt90) cc_final: 0.7870 (ttt90) REVERT: R 390 LEU cc_start: 0.8538 (mp) cc_final: 0.8218 (mm) REVERT: R 439 ASN cc_start: 0.8241 (t0) cc_final: 0.7936 (t0) outliers start: 27 outliers final: 21 residues processed: 181 average time/residue: 0.1975 time to fit residues: 48.7354 Evaluate side-chains 191 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 109 THR 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 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 63 SER Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 9 SER 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 9 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105672 restraints weight = 12905.924| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.28 r_work: 0.3262 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8627 Z= 0.143 Angle : 0.577 10.026 11745 Z= 0.295 Chirality : 0.043 0.166 1297 Planarity : 0.004 0.042 1498 Dihedral : 6.988 101.506 1272 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.50 % Allowed : 15.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1076 helix: -2.63 (0.64), residues: 39 sheet: 0.45 (0.25), residues: 474 loop : -0.44 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 353 HIS 0.003 0.001 HIS A 214 PHE 0.013 0.001 PHE R 456 TYR 0.021 0.001 TYR C 105 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 1) link_NAG-ASN : angle 2.10059 ( 3) link_BETA1-4 : bond 0.00543 ( 2) link_BETA1-4 : angle 1.82362 ( 6) hydrogen bonds : bond 0.03682 ( 275) hydrogen bonds : angle 5.83044 ( 768) link_BETA1-6 : bond 0.01141 ( 1) link_BETA1-6 : angle 1.89902 ( 3) SS BOND : bond 0.00783 ( 12) SS BOND : angle 1.89003 ( 24) covalent geometry : bond 0.00332 ( 8611) covalent geometry : angle 0.56779 (11709) *********************** 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 186 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.934 Fit side-chains REVERT: A 127 SER cc_start: 0.8345 (t) cc_final: 0.8065 (p) REVERT: A 129 SER cc_start: 0.8654 (t) cc_final: 0.8373 (p) REVERT: A 157 LYS cc_start: 0.7664 (ttmm) cc_final: 0.7262 (ttmm) REVERT: B 163 VAL cc_start: 0.8818 (t) cc_final: 0.8497 (p) REVERT: B 183 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7306 (ttmt) REVERT: H 84 SER cc_start: 0.8826 (m) cc_final: 0.8482 (t) REVERT: L 4 MET cc_start: 0.7588 (mmm) cc_final: 0.6785 (mmm) REVERT: L 104 LYS cc_start: 0.8487 (tttt) cc_final: 0.8192 (tttp) REVERT: R 354 ASN cc_start: 0.8519 (t0) cc_final: 0.8181 (t0) REVERT: R 357 ARG cc_start: 0.8139 (ttt90) cc_final: 0.7825 (ttt90) REVERT: R 439 ASN cc_start: 0.8276 (t0) cc_final: 0.7963 (t0) outliers start: 23 outliers final: 19 residues processed: 172 average time/residue: 0.1918 time to fit residues: 45.9640 Evaluate side-chains 180 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 132 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 D residue 5 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 9 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 104 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.0060 chunk 99 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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** 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 = 0.3680 r_free = 0.3680 target = 0.126312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106961 restraints weight = 12832.269| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.18 r_work: 0.3282 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8627 Z= 0.133 Angle : 0.556 8.591 11745 Z= 0.284 Chirality : 0.043 0.154 1297 Planarity : 0.004 0.041 1498 Dihedral : 6.802 99.145 1272 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.95 % Allowed : 16.07 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1076 helix: -2.52 (0.66), residues: 39 sheet: 0.50 (0.25), residues: 474 loop : -0.41 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 353 HIS 0.003 0.001 HIS A 214 PHE 0.012 0.001 PHE R 456 TYR 0.016 0.001 TYR C 105 ARG 0.002 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 1) link_NAG-ASN : angle 1.93545 ( 3) link_BETA1-4 : bond 0.00396 ( 2) link_BETA1-4 : angle 1.76702 ( 6) hydrogen bonds : bond 0.03457 ( 275) hydrogen bonds : angle 5.67110 ( 768) link_BETA1-6 : bond 0.01062 ( 1) link_BETA1-6 : angle 1.95924 ( 3) SS BOND : bond 0.00711 ( 12) SS BOND : angle 1.77750 ( 24) covalent geometry : bond 0.00308 ( 8611) covalent geometry : angle 0.54797 (11709) *********************** 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 184 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.917 Fit side-chains REVERT: A 127 SER cc_start: 0.8308 (t) cc_final: 0.8036 (p) REVERT: A 129 SER cc_start: 0.8644 (t) cc_final: 0.8353 (p) REVERT: A 157 LYS cc_start: 0.7650 (ttmm) cc_final: 0.7275 (ttmm) REVERT: H 84 SER cc_start: 0.8820 (m) cc_final: 0.8484 (t) REVERT: L 4 MET cc_start: 0.7540 (mmm) cc_final: 0.6751 (mmm) REVERT: L 104 LYS cc_start: 0.8467 (tttt) cc_final: 0.8167 (tttp) REVERT: R 354 ASN cc_start: 0.8445 (t0) cc_final: 0.8111 (t0) REVERT: R 357 ARG cc_start: 0.8105 (ttt90) cc_final: 0.7653 (ttt90) REVERT: R 394 ASN cc_start: 0.7577 (m-40) cc_final: 0.6729 (m-40) REVERT: R 439 ASN cc_start: 0.8309 (t0) cc_final: 0.7975 (t0) outliers start: 18 outliers final: 16 residues processed: 171 average time/residue: 0.1951 time to fit residues: 46.2977 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 : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 205 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 6 GLN ** 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 = 0.3675 r_free = 0.3675 target = 0.125708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106388 restraints weight = 12708.251| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.16 r_work: 0.3279 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8627 Z= 0.153 Angle : 0.573 8.881 11745 Z= 0.290 Chirality : 0.043 0.154 1297 Planarity : 0.004 0.040 1498 Dihedral : 6.829 99.567 1272 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.28 % Allowed : 16.07 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1076 helix: -2.50 (0.66), residues: 39 sheet: 0.50 (0.25), residues: 474 loop : -0.41 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 353 HIS 0.003 0.001 HIS B 92 PHE 0.014 0.001 PHE R 456 TYR 0.016 0.001 TYR C 105 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 1) link_NAG-ASN : angle 2.03138 ( 3) link_BETA1-4 : bond 0.00470 ( 2) link_BETA1-4 : angle 1.82378 ( 6) hydrogen bonds : bond 0.03583 ( 275) hydrogen bonds : angle 5.67212 ( 768) link_BETA1-6 : bond 0.01099 ( 1) link_BETA1-6 : angle 1.96909 ( 3) SS BOND : bond 0.00746 ( 12) SS BOND : angle 1.76253 ( 24) covalent geometry : bond 0.00357 ( 8611) covalent geometry : angle 0.56477 (11709) ********************** 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 186 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.848 Fit side-chains REVERT: A 127 SER cc_start: 0.8290 (t) cc_final: 0.8027 (p) REVERT: A 129 SER cc_start: 0.8633 (t) cc_final: 0.8342 (p) REVERT: A 157 LYS cc_start: 0.7655 (ttmm) cc_final: 0.7278 (ttmm) REVERT: H 84 SER cc_start: 0.8821 (m) cc_final: 0.8483 (t) REVERT: L 4 MET cc_start: 0.7543 (mmm) cc_final: 0.6749 (mmm) REVERT: L 104 LYS cc_start: 0.8463 (tttt) cc_final: 0.8164 (tttp) REVERT: R 354 ASN cc_start: 0.8459 (t0) cc_final: 0.8124 (t0) REVERT: R 357 ARG cc_start: 0.8083 (ttt90) cc_final: 0.7597 (ttt90) REVERT: R 394 ASN cc_start: 0.7579 (m-40) cc_final: 0.6733 (m-40) REVERT: R 439 ASN cc_start: 0.8287 (t0) cc_final: 0.7943 (t0) outliers start: 21 outliers final: 18 residues processed: 173 average time/residue: 0.1972 time to fit residues: 47.1493 Evaluate side-chains 183 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL 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 5 THR Chi-restraints excluded: chain H residue 7 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 43 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 26 optimal weight: 0.0670 chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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** H 3 GLN 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 = 0.126093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106721 restraints weight = 12904.363| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.18 r_work: 0.3282 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2372 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= 0.132 Angle : 0.569 8.784 11745 Z= 0.289 Chirality : 0.043 0.153 1297 Planarity : 0.004 0.042 1498 Dihedral : 6.780 98.863 1272 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.17 % Allowed : 16.40 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1076 helix: -2.45 (0.67), residues: 39 sheet: 0.50 (0.25), residues: 474 loop : -0.40 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 353 HIS 0.004 0.001 HIS B 92 PHE 0.012 0.001 PHE R 456 TYR 0.015 0.001 TYR C 105 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 1) link_NAG-ASN : angle 1.99130 ( 3) link_BETA1-4 : bond 0.00488 ( 2) link_BETA1-4 : angle 1.78443 ( 6) hydrogen bonds : bond 0.03457 ( 275) hydrogen bonds : angle 5.64896 ( 768) link_BETA1-6 : bond 0.01110 ( 1) link_BETA1-6 : angle 1.98125 ( 3) SS BOND : bond 0.00711 ( 12) SS BOND : angle 2.32872 ( 24) covalent geometry : bond 0.00306 ( 8611) covalent geometry : angle 0.55699 (11709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5010.25 seconds wall clock time: 87 minutes 15.94 seconds (5235.94 seconds total)