Starting phenix.real_space_refine on Sat Dec 28 11:32:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpy_37726/12_2024/8wpy_37726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpy_37726/12_2024/8wpy_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_37726/12_2024/8wpy_37726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpy_37726/12_2024/8wpy_37726.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpy_37726/12_2024/8wpy_37726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpy_37726/12_2024/8wpy_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.84, per 1000 atoms: 0.69 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: 2.41 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: 1.53 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: 3.33 Time building geometry restraints manager: 2.72 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: 2.880 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.310 Find NCS groups from input model: 0.170 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.800 ------------------------------------------------------------------------------- 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 8611 Z= 0.165 Angle : 0.504 6.334 11709 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 *********************** 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 : 0.946 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: 0.2058 time to fit residues: 64.5826 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 : 1.016 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 8611 Z= 0.272 Angle : 0.589 8.927 11709 Z= 0.307 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 *********************** 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 : 0.915 Fit side-chains REVERT: A 127 SER cc_start: 0.8293 (t) cc_final: 0.7959 (p) REVERT: A 129 SER cc_start: 0.8295 (t) cc_final: 0.8029 (p) REVERT: B 27 GLN cc_start: 0.8150 (mt0) cc_final: 0.7923 (mt0) REVERT: B 118 PHE cc_start: 0.8959 (m-80) cc_final: 0.8462 (m-80) REVERT: B 136 LEU cc_start: 0.8548 (mp) cc_final: 0.8323 (mp) REVERT: B 163 VAL cc_start: 0.8687 (t) cc_final: 0.8283 (p) REVERT: B 176 SER cc_start: 0.7981 (t) cc_final: 0.7702 (m) REVERT: B 183 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6993 (ttmt) REVERT: C 66 ARG cc_start: 0.8622 (mtm110) cc_final: 0.8300 (mtp180) REVERT: D 71 PHE cc_start: 0.7868 (m-80) cc_final: 0.7592 (m-80) REVERT: H 84 SER cc_start: 0.8725 (m) cc_final: 0.8388 (t) REVERT: L 4 MET cc_start: 0.7102 (mmm) cc_final: 0.6252 (mmm) REVERT: R 357 ARG cc_start: 0.7141 (ttt90) cc_final: 0.6761 (ttt90) REVERT: R 394 ASN cc_start: 0.7325 (m-40) cc_final: 0.6295 (m-40) REVERT: R 439 ASN cc_start: 0.8017 (t0) cc_final: 0.7639 (t0) outliers start: 16 outliers final: 12 residues processed: 193 average time/residue: 0.2152 time to fit residues: 56.5705 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 : 0.994 ------------------------------------------------------------------------------- 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 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8611 Z= 0.255 Angle : 0.570 8.372 11709 Z= 0.295 Chirality : 0.044 0.154 1297 Planarity : 0.004 0.037 1498 Dihedral : 7.690 104.475 1273 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.26 % Allowed : 12.60 % 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: -0.02 (0.26), residues: 1076 helix: -2.84 (0.54), residues: 46 sheet: 0.67 (0.25), residues: 466 loop : -0.29 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.004 0.001 HIS B 92 PHE 0.015 0.002 PHE R 456 TYR 0.018 0.002 TYR H 79 ARG 0.003 0.000 ARG H 71 *********************** 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 205 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.889 Fit side-chains REVERT: A 127 SER cc_start: 0.8251 (t) cc_final: 0.7910 (p) REVERT: A 129 SER cc_start: 0.8321 (t) cc_final: 0.8048 (p) REVERT: B 27 GLN cc_start: 0.8184 (mt0) cc_final: 0.7966 (mt0) REVERT: B 118 PHE cc_start: 0.8898 (m-80) cc_final: 0.8465 (m-80) REVERT: B 163 VAL cc_start: 0.8664 (t) cc_final: 0.8274 (p) REVERT: B 176 SER cc_start: 0.7924 (t) cc_final: 0.7634 (m) REVERT: C 66 ARG cc_start: 0.8627 (mtm110) cc_final: 0.8321 (mtp180) REVERT: D 71 PHE cc_start: 0.7915 (m-80) cc_final: 0.7601 (m-80) REVERT: H 84 SER cc_start: 0.8742 (m) cc_final: 0.8423 (t) REVERT: L 4 MET cc_start: 0.7034 (mmm) cc_final: 0.6299 (mmm) REVERT: R 357 ARG cc_start: 0.7160 (ttt90) cc_final: 0.6790 (ttt90) REVERT: R 390 LEU cc_start: 0.8508 (mp) cc_final: 0.8272 (mm) REVERT: R 394 ASN cc_start: 0.7325 (m-40) cc_final: 0.6315 (m-40) REVERT: R 439 ASN cc_start: 0.8050 (t0) cc_final: 0.7676 (t0) outliers start: 30 outliers final: 21 residues processed: 188 average time/residue: 0.2036 time to fit residues: 52.6661 Evaluate side-chains 195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 45 LYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8611 Z= 0.267 Angle : 0.565 7.321 11709 Z= 0.294 Chirality : 0.043 0.153 1297 Planarity : 0.004 0.035 1498 Dihedral : 7.314 103.611 1273 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.39 % Allowed : 13.25 % Favored : 84.36 % 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: -0.09 (0.26), residues: 1076 helix: -2.82 (0.54), residues: 46 sheet: 0.61 (0.25), residues: 466 loop : -0.32 (0.26), residues: 564 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 0.016 0.001 PHE R 392 TYR 0.019 0.002 TYR C 105 ARG 0.003 0.000 ARG H 71 *********************** 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 196 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.870 Fit side-chains REVERT: A 115 ASP cc_start: 0.7741 (p0) cc_final: 0.7485 (p0) REVERT: A 127 SER cc_start: 0.8222 (t) cc_final: 0.7880 (p) REVERT: A 129 SER cc_start: 0.8328 (t) cc_final: 0.8058 (p) REVERT: A 157 LYS cc_start: 0.7465 (ttmm) cc_final: 0.7098 (ttmm) REVERT: B 27 GLN cc_start: 0.8175 (mt0) cc_final: 0.7971 (mt0) REVERT: B 118 PHE cc_start: 0.8914 (m-80) cc_final: 0.8524 (m-80) REVERT: B 163 VAL cc_start: 0.8689 (t) cc_final: 0.8302 (p) REVERT: B 176 SER cc_start: 0.7988 (t) cc_final: 0.7677 (m) REVERT: H 84 SER cc_start: 0.8754 (m) cc_final: 0.8450 (t) REVERT: R 357 ARG cc_start: 0.7165 (ttt90) cc_final: 0.6786 (ttt90) REVERT: R 390 LEU cc_start: 0.8538 (mp) cc_final: 0.8329 (mm) REVERT: R 394 ASN cc_start: 0.7358 (m-40) cc_final: 0.6328 (m-40) REVERT: R 439 ASN cc_start: 0.8014 (t0) cc_final: 0.7668 (t0) outliers start: 22 outliers final: 16 residues processed: 183 average time/residue: 0.2178 time to fit residues: 54.3312 Evaluate side-chains 189 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 84 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8611 Z= 0.296 Angle : 0.571 7.549 11709 Z= 0.298 Chirality : 0.044 0.149 1297 Planarity : 0.004 0.037 1498 Dihedral : 7.175 102.654 1273 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.61 % Allowed : 14.55 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.81 (0.55), residues: 46 sheet: 0.55 (0.25), residues: 462 loop : -0.30 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 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 0.002 0.000 ARG H 71 *********************** 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 200 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.850 Fit side-chains REVERT: A 115 ASP cc_start: 0.7739 (p0) cc_final: 0.7479 (p0) REVERT: A 127 SER cc_start: 0.8193 (t) cc_final: 0.7841 (p) REVERT: A 129 SER cc_start: 0.8310 (t) cc_final: 0.8040 (p) REVERT: A 157 LYS cc_start: 0.7450 (ttmm) cc_final: 0.7052 (ttmm) REVERT: B 118 PHE cc_start: 0.8902 (m-80) cc_final: 0.8522 (m-80) REVERT: B 163 VAL cc_start: 0.8632 (t) cc_final: 0.8266 (p) REVERT: B 176 SER cc_start: 0.7998 (t) cc_final: 0.7681 (m) REVERT: B 183 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7224 (ttmt) REVERT: H 84 SER cc_start: 0.8750 (m) cc_final: 0.8460 (t) REVERT: L 4 MET cc_start: 0.7256 (mmm) cc_final: 0.6350 (mmm) REVERT: R 354 ASN cc_start: 0.8231 (t0) cc_final: 0.7880 (t0) REVERT: R 357 ARG cc_start: 0.7158 (ttt90) cc_final: 0.6892 (ttt90) REVERT: R 439 ASN cc_start: 0.7988 (t0) cc_final: 0.7645 (t0) outliers start: 24 outliers final: 17 residues processed: 185 average time/residue: 0.2083 time to fit residues: 53.3854 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 : 0.967 ------------------------------------------------------------------------------- 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 A residue 210 CYS 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 183 LYS Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 0.3980 chunk 20 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** R 440 ASN R 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8611 Z= 0.197 Angle : 0.549 12.009 11709 Z= 0.283 Chirality : 0.043 0.200 1297 Planarity : 0.004 0.036 1498 Dihedral : 6.930 99.655 1273 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.74 % Allowed : 15.85 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.26), residues: 1076 helix: -2.72 (0.56), residues: 46 sheet: 0.57 (0.25), residues: 474 loop : -0.28 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 353 HIS 0.002 0.001 HIS A 214 PHE 0.012 0.001 PHE R 392 TYR 0.019 0.001 TYR H 79 ARG 0.002 0.000 ARG H 71 *********************** 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 187 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.965 Fit side-chains REVERT: A 127 SER cc_start: 0.8144 (t) cc_final: 0.7792 (p) REVERT: A 129 SER cc_start: 0.8313 (t) cc_final: 0.8044 (p) REVERT: A 157 LYS cc_start: 0.7413 (ttmm) cc_final: 0.7101 (ttmm) REVERT: B 176 SER cc_start: 0.7908 (t) cc_final: 0.7618 (m) REVERT: C 66 ARG cc_start: 0.8615 (mtm110) cc_final: 0.8348 (mtp180) REVERT: H 84 SER cc_start: 0.8752 (m) cc_final: 0.8479 (t) REVERT: L 4 MET cc_start: 0.7183 (mmm) cc_final: 0.6330 (mmm) REVERT: R 354 ASN cc_start: 0.8188 (t0) cc_final: 0.7847 (t0) REVERT: R 357 ARG cc_start: 0.7140 (ttt90) cc_final: 0.6877 (ttt90) REVERT: R 439 ASN cc_start: 0.7970 (t0) cc_final: 0.7648 (t0) outliers start: 16 outliers final: 12 residues processed: 178 average time/residue: 0.2173 time to fit residues: 52.5807 Evaluate side-chains 178 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL 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 117 ILE 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 D residue 5 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN D 34 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8611 Z= 0.220 Angle : 0.554 10.411 11709 Z= 0.285 Chirality : 0.043 0.164 1297 Planarity : 0.004 0.038 1498 Dihedral : 6.774 99.569 1272 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.17 % Allowed : 15.64 % Favored : 82.19 % 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: -0.08 (0.26), residues: 1076 helix: -2.73 (0.57), residues: 46 sheet: 0.54 (0.25), residues: 474 loop : -0.25 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 110 HIS 0.004 0.001 HIS B 92 PHE 0.013 0.001 PHE R 456 TYR 0.019 0.001 TYR H 79 ARG 0.002 0.000 ARG H 71 *********************** 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 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.965 Fit side-chains REVERT: A 127 SER cc_start: 0.8118 (t) cc_final: 0.7759 (p) REVERT: A 129 SER cc_start: 0.8321 (t) cc_final: 0.8050 (p) REVERT: A 157 LYS cc_start: 0.7434 (ttmm) cc_final: 0.7111 (ttmm) REVERT: B 163 VAL cc_start: 0.8605 (t) cc_final: 0.8231 (p) REVERT: B 176 SER cc_start: 0.7975 (t) cc_final: 0.7684 (m) REVERT: C 66 ARG cc_start: 0.8615 (mtm110) cc_final: 0.8359 (mtp180) REVERT: H 84 SER cc_start: 0.8750 (m) cc_final: 0.8483 (t) REVERT: L 4 MET cc_start: 0.7180 (mmm) cc_final: 0.6566 (mtp) REVERT: R 354 ASN cc_start: 0.8207 (t0) cc_final: 0.7858 (t0) REVERT: R 357 ARG cc_start: 0.7139 (ttt90) cc_final: 0.6879 (ttt90) REVERT: R 390 LEU cc_start: 0.8571 (mp) cc_final: 0.8270 (mm) REVERT: R 439 ASN cc_start: 0.8012 (t0) cc_final: 0.7684 (t0) outliers start: 20 outliers final: 18 residues processed: 179 average time/residue: 0.2117 time to fit residues: 52.0547 Evaluate side-chains 189 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 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 96 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8611 Z= 0.277 Angle : 0.573 9.130 11709 Z= 0.296 Chirality : 0.044 0.154 1297 Planarity : 0.004 0.040 1498 Dihedral : 6.912 101.149 1272 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.39 % Allowed : 14.98 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.26), residues: 1076 helix: -2.75 (0.57), residues: 46 sheet: 0.48 (0.25), residues: 475 loop : -0.29 (0.26), residues: 555 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 0.015 0.001 PHE R 456 TYR 0.020 0.002 TYR H 79 ARG 0.003 0.000 ARG B 46 *********************** 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 195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 127 SER cc_start: 0.8094 (t) cc_final: 0.7845 (p) REVERT: A 129 SER cc_start: 0.8339 (t) cc_final: 0.8077 (p) REVERT: A 157 LYS cc_start: 0.7453 (ttmm) cc_final: 0.7146 (ttmm) REVERT: B 163 VAL cc_start: 0.8589 (t) cc_final: 0.8214 (p) REVERT: B 175 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8203 (mp) REVERT: B 176 SER cc_start: 0.7961 (t) cc_final: 0.7656 (m) REVERT: C 49 SER cc_start: 0.8505 (t) cc_final: 0.8241 (p) REVERT: H 84 SER cc_start: 0.8749 (m) cc_final: 0.8487 (t) REVERT: L 4 MET cc_start: 0.7211 (mmm) cc_final: 0.6556 (mtm) REVERT: R 354 ASN cc_start: 0.8216 (t0) cc_final: 0.7849 (t0) REVERT: R 357 ARG cc_start: 0.7147 (ttt90) cc_final: 0.6837 (ttt90) REVERT: R 439 ASN cc_start: 0.8011 (t0) cc_final: 0.7683 (t0) outliers start: 22 outliers final: 16 residues processed: 183 average time/residue: 0.2026 time to fit residues: 51.4870 Evaluate side-chains 189 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 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** C 76 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8611 Z= 0.230 Angle : 0.552 8.636 11709 Z= 0.285 Chirality : 0.043 0.150 1297 Planarity : 0.004 0.038 1498 Dihedral : 6.828 100.015 1272 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.17 % Allowed : 15.31 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.26), residues: 1076 helix: -2.69 (0.57), residues: 46 sheet: 0.49 (0.25), residues: 475 loop : -0.28 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 353 HIS 0.003 0.001 HIS B 92 PHE 0.013 0.001 PHE R 456 TYR 0.021 0.001 TYR C 105 ARG 0.003 0.000 ARG H 71 *********************** 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 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.024 Fit side-chains REVERT: A 127 SER cc_start: 0.8064 (t) cc_final: 0.7820 (p) REVERT: A 129 SER cc_start: 0.8346 (t) cc_final: 0.8078 (p) REVERT: A 157 LYS cc_start: 0.7420 (ttmm) cc_final: 0.7118 (ttmm) REVERT: B 163 VAL cc_start: 0.8538 (t) cc_final: 0.8162 (p) REVERT: B 176 SER cc_start: 0.7942 (t) cc_final: 0.7659 (m) REVERT: C 66 ARG cc_start: 0.8614 (mtm110) cc_final: 0.8363 (mtp180) REVERT: H 84 SER cc_start: 0.8749 (m) cc_final: 0.8510 (t) REVERT: L 4 MET cc_start: 0.7186 (mmm) cc_final: 0.6541 (mtp) REVERT: R 354 ASN cc_start: 0.8148 (t0) cc_final: 0.7776 (t0) REVERT: R 357 ARG cc_start: 0.7137 (ttt90) cc_final: 0.6635 (ttt90) REVERT: R 394 ASN cc_start: 0.7286 (m-40) cc_final: 0.6190 (m-40) REVERT: R 439 ASN cc_start: 0.8018 (t0) cc_final: 0.7694 (t0) outliers start: 20 outliers final: 19 residues processed: 179 average time/residue: 0.2165 time to fit residues: 52.8246 Evaluate side-chains 188 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 107 LYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 53 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 0.0050 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8611 Z= 0.173 Angle : 0.541 8.973 11709 Z= 0.277 Chirality : 0.043 0.150 1297 Planarity : 0.004 0.041 1498 Dihedral : 6.685 97.991 1272 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.85 % Allowed : 15.74 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.26), residues: 1076 helix: -2.64 (0.58), residues: 46 sheet: 0.53 (0.25), residues: 474 loop : -0.27 (0.26), residues: 556 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 0.010 0.001 PHE R 456 TYR 0.020 0.001 TYR H 79 ARG 0.003 0.000 ARG D 61 ********************** 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 189 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 127 SER cc_start: 0.8042 (t) cc_final: 0.7799 (p) REVERT: A 129 SER cc_start: 0.8341 (t) cc_final: 0.8070 (p) REVERT: A 157 LYS cc_start: 0.7399 (ttmm) cc_final: 0.7098 (ttmm) REVERT: B 163 VAL cc_start: 0.8524 (t) cc_final: 0.8154 (p) REVERT: B 176 SER cc_start: 0.7914 (t) cc_final: 0.7632 (m) REVERT: C 66 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8366 (mtp180) REVERT: H 84 SER cc_start: 0.8762 (m) cc_final: 0.8532 (t) REVERT: L 4 MET cc_start: 0.7139 (mmm) cc_final: 0.6567 (mtp) REVERT: R 354 ASN cc_start: 0.8111 (t0) cc_final: 0.7749 (t0) REVERT: R 357 ARG cc_start: 0.7113 (ttt90) cc_final: 0.6816 (ttt90) REVERT: R 439 ASN cc_start: 0.8016 (t0) cc_final: 0.7680 (t0) outliers start: 17 outliers final: 16 residues processed: 180 average time/residue: 0.2112 time to fit residues: 52.1179 Evaluate side-chains 186 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 117 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain D residue 5 THR 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 392 PHE 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 88 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 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 90 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN D 6 GLN ** 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 = 0.3673 r_free = 0.3673 target = 0.125704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106417 restraints weight = 12745.016| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.15 r_work: 0.3272 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8611 Z= 0.271 Angle : 0.573 9.010 11709 Z= 0.294 Chirality : 0.044 0.149 1297 Planarity : 0.004 0.042 1498 Dihedral : 6.831 99.783 1272 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.95 % Allowed : 16.29 % Favored : 81.76 % 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 (0.26), residues: 1076 helix: -2.66 (0.58), residues: 46 sheet: 0.48 (0.25), residues: 475 loop : -0.28 (0.26), residues: 555 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 0.020 0.001 PHE A 29 TYR 0.020 0.002 TYR H 79 ARG 0.003 0.000 ARG H 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.96 seconds wall clock time: 42 minutes 50.28 seconds (2570.28 seconds total)