Starting phenix.real_space_refine on Tue Feb 3 23:18:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z4o_39768/02_2026/8z4o_39768_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z4o_39768/02_2026/8z4o_39768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z4o_39768/02_2026/8z4o_39768_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z4o_39768/02_2026/8z4o_39768_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z4o_39768/02_2026/8z4o_39768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z4o_39768/02_2026/8z4o_39768.map" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4709 2.51 5 N 1233 2.21 5 O 1540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "A GLU 1183": not complete - not flipped Residue "A GLU 1237": not complete - not flipped Residue "B GLU 1183": not complete - not flipped Residue "B GLU 1237": not complete - not flipped Residue "C GLU 1183": not complete - not flipped Residue "C GLU 1237": not complete - not flipped Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7515 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2439 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 12, 'TRANS': 345} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 21, 'TYR:plan': 9, 'ASN:plan1': 13, 'GLU:plan': 7, 'ARG:plan': 3, 'HIS:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 211 Chain: "B" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2437 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 12, 'TRANS': 345} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 21, 'TYR:plan': 9, 'ASN:plan1': 13, 'GLU:plan': 7, 'ARG:plan': 2, 'HIS:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 203 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2415 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 12, 'TRANS': 344} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 21, 'TYR:plan': 9, 'ASN:plan1': 13, 'GLU:plan': 8, 'ARG:plan': 3, 'HIS:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 212 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.76, per 1000 atoms: 0.23 Number of scatterers: 7515 At special positions: 0 Unit cell: (78.4166, 78.4166, 215.914, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1540 8.00 N 1233 7.00 C 4709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.02 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.02 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.02 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.02 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.01 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.00 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.05 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.18 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=1.99 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.01 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.04 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 NAG-ASN " NAG A1301 " - " ASN A 785 " " NAG A1302 " - " ASN A1225 " " NAG A1303 " - " ASN A1241 " " NAG A1304 " - " ASN A1277 " " NAG A1305 " - " ASN A1160 " " NAG B1301 " - " ASN B 785 " " NAG B1302 " - " ASN B1225 " " NAG B1303 " - " ASN B1241 " " NAG B1304 " - " ASN B1256 " " NAG B1305 " - " ASN B1277 " " NAG C1301 " - " ASN C 785 " " NAG C1302 " - " ASN C1225 " " NAG C1303 " - " ASN C1241 " " NAG C1304 " - " ASN C1277 " " NAG C1305 " - " ASN C 774 " " NAG C1306 " - " ASN C1160 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 231.7 milliseconds 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 9 sheets defined 49.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 814 through 825 removed outlier: 3.571A pdb=" N GLU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 838 removed outlier: 3.600A pdb=" N ALA A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1106 removed outlier: 3.632A pdb=" N GLN A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1239 removed outlier: 4.155A pdb=" N PHE A1238 " --> pdb=" O GLU A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1280 Processing helix chain 'B' and resid 805 through 811 Processing helix chain 'B' and resid 814 through 825 removed outlier: 3.956A pdb=" N GLU B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 838 removed outlier: 3.646A pdb=" N ALA B 838 " --> pdb=" O ALA B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 1106 removed outlier: 3.655A pdb=" N GLN B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1239 removed outlier: 4.169A pdb=" N PHE B1238 " --> pdb=" O GLU B1234 " (cutoff:3.500A) Processing helix chain 'B' and resid 1264 through 1277 Processing helix chain 'C' and resid 805 through 811 Processing helix chain 'C' and resid 814 through 825 removed outlier: 3.832A pdb=" N GLU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 838 removed outlier: 3.659A pdb=" N ALA C 838 " --> pdb=" O ALA C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1106 removed outlier: 3.719A pdb=" N GLN C1066 " --> pdb=" O GLU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1239 removed outlier: 3.515A pdb=" N GLU C1234 " --> pdb=" O ASP C1230 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE C1238 " --> pdb=" O GLU C1234 " (cutoff:3.500A) Processing helix chain 'C' and resid 1264 through 1280 Processing sheet with id=AA1, first strand: chain 'A' and resid 1124 through 1126 removed outlier: 4.729A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1124 through 1126 removed outlier: 6.683A pdb=" N ASN A 785 " --> pdb=" O SER A1144 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA A1152 " --> pdb=" O TYR A 777 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR A 777 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N TYR B1211 " --> pdb=" O PHE A 786 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE A 788 " --> pdb=" O TYR B1211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1164 through 1167 removed outlier: 3.842A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A1166 " --> pdb=" O LYS A1203 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A1203 " --> pdb=" O ALA A1166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1211 through 1212 removed outlier: 7.023A pdb=" N TYR C 777 " --> pdb=" O ALA C1152 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA C1152 " --> pdb=" O TYR C 777 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS C 779 " --> pdb=" O VAL C1150 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL C1150 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER C 781 " --> pdb=" O GLU C1148 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU C1148 " --> pdb=" O SER C 781 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N HIS C1146 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN C 785 " --> pdb=" O SER C1144 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C1126 " --> pdb=" O MET C1137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1211 through 1212 removed outlier: 7.023A pdb=" N TYR C 777 " --> pdb=" O ALA C1152 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA C1152 " --> pdb=" O TYR C 777 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS C 779 " --> pdb=" O VAL C1150 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL C1150 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER C 781 " --> pdb=" O GLU C1148 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU C1148 " --> pdb=" O SER C 781 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N HIS C1146 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN C 785 " --> pdb=" O SER C1144 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1124 through 1129 removed outlier: 4.140A pdb=" N PHE B1126 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1124 through 1129 removed outlier: 4.140A pdb=" N PHE B1126 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN B 785 " --> pdb=" O SER B1144 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N HIS B1146 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU B1148 " --> pdb=" O SER B 781 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER B 781 " --> pdb=" O GLU B1148 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL B1150 " --> pdb=" O LYS B 779 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS B 779 " --> pdb=" O VAL B1150 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA B1152 " --> pdb=" O TYR B 777 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR B 777 " --> pdb=" O ALA B1152 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N TYR C1211 " --> pdb=" O PHE B 786 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE B 788 " --> pdb=" O TYR C1211 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1164 through 1167 removed outlier: 3.814A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B1166 " --> pdb=" O LYS B1203 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B1203 " --> pdb=" O ALA B1166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1164 through 1167 removed outlier: 3.834A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA C1166 " --> pdb=" O LYS C1203 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS C1203 " --> pdb=" O ALA C1166 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1545 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: 0.94 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1310 1.31 - 1.44: 1866 1.44 - 1.56: 4384 1.56 - 1.69: 0 1.69 - 1.82: 33 Bond restraints: 7593 Sorted by residual: bond pdb=" N PRO A1167 " pdb=" CD PRO A1167 " ideal model delta sigma weight residual 1.473 1.231 0.242 1.40e-02 5.10e+03 2.99e+02 bond pdb=" N PRO C1167 " pdb=" CD PRO C1167 " ideal model delta sigma weight residual 1.473 1.269 0.204 1.40e-02 5.10e+03 2.13e+02 bond pdb=" N PRO B1167 " pdb=" CD PRO B1167 " ideal model delta sigma weight residual 1.473 1.288 0.185 1.40e-02 5.10e+03 1.74e+02 bond pdb=" N PRO B1161 " pdb=" CD PRO B1161 " ideal model delta sigma weight residual 1.473 1.374 0.099 1.40e-02 5.10e+03 4.97e+01 bond pdb=" N CYS A 811 " pdb=" CA CYS A 811 " ideal model delta sigma weight residual 1.458 1.487 -0.028 6.30e-03 2.52e+04 2.03e+01 ... (remaining 7588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 9616 4.07 - 8.14: 583 8.14 - 12.20: 29 12.20 - 16.27: 3 16.27 - 20.34: 4 Bond angle restraints: 10235 Sorted by residual: angle pdb=" C PRO B1167 " pdb=" CA PRO B1167 " pdb=" CB PRO B1167 " ideal model delta sigma weight residual 111.64 91.30 20.34 1.26e+00 6.30e-01 2.61e+02 angle pdb=" C PRO A1167 " pdb=" CA PRO A1167 " pdb=" CB PRO A1167 " ideal model delta sigma weight residual 111.64 92.23 19.41 1.26e+00 6.30e-01 2.37e+02 angle pdb=" C PRO C1167 " pdb=" CA PRO C1167 " pdb=" CB PRO C1167 " ideal model delta sigma weight residual 111.46 93.09 18.37 1.29e+00 6.01e-01 2.03e+02 angle pdb=" N PRO A1167 " pdb=" CA PRO A1167 " pdb=" CB PRO A1167 " ideal model delta sigma weight residual 103.27 94.82 8.45 9.00e-01 1.23e+00 8.81e+01 angle pdb=" N PRO C1161 " pdb=" CA PRO C1161 " pdb=" C PRO C1161 " ideal model delta sigma weight residual 111.03 124.91 -13.88 1.54e+00 4.22e-01 8.12e+01 ... (remaining 10230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 4757 35.10 - 70.20: 112 70.20 - 105.30: 6 105.30 - 140.40: 0 140.40 - 175.50: 9 Dihedral angle restraints: 4884 sinusoidal: 1779 harmonic: 3105 Sorted by residual: dihedral pdb=" C PRO B1167 " pdb=" N PRO B1167 " pdb=" CA PRO B1167 " pdb=" CB PRO B1167 " ideal model delta harmonic sigma weight residual -120.70 -93.87 -26.83 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" C PRO A1167 " pdb=" N PRO A1167 " pdb=" CA PRO A1167 " pdb=" CB PRO A1167 " ideal model delta harmonic sigma weight residual -120.70 -94.29 -26.41 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" C PRO C1167 " pdb=" N PRO C1167 " pdb=" CA PRO C1167 " pdb=" CB PRO C1167 " ideal model delta harmonic sigma weight residual -120.70 -95.89 -24.81 0 2.50e+00 1.60e-01 9.85e+01 ... (remaining 4881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 643 0.113 - 0.225: 468 0.225 - 0.338: 107 0.338 - 0.450: 20 0.450 - 0.563: 5 Chirality restraints: 1243 Sorted by residual: chirality pdb=" CA ASN C1160 " pdb=" N ASN C1160 " pdb=" C ASN C1160 " pdb=" CB ASN C1160 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A1160 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.34e+00 chirality pdb=" CA ASN B 774 " pdb=" N ASN B 774 " pdb=" C ASN B 774 " pdb=" CB ASN B 774 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.37e+00 ... (remaining 1240 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " -0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG A1305 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " -0.144 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " -0.344 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B1303 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " -0.159 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " 0.521 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.323 2.00e-02 2.50e+03 2.82e-01 9.91e+02 pdb=" C7 NAG A1301 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.503 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.149 2.00e-02 2.50e+03 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 520 2.70 - 3.25: 8225 3.25 - 3.80: 11375 3.80 - 4.35: 14525 4.35 - 4.90: 21993 Nonbonded interactions: 56638 Sorted by model distance: nonbonded pdb=" O THR A1010 " pdb=" OG1 THR A1013 " model vdw 2.155 3.040 nonbonded pdb=" N PRO B1196 " pdb=" CG PRO B1196 " model vdw 2.183 2.816 nonbonded pdb=" N PRO C1196 " pdb=" CG PRO C1196 " model vdw 2.185 2.816 nonbonded pdb=" N PRO A1196 " pdb=" CG PRO A1196 " model vdw 2.198 2.816 nonbonded pdb=" N PRO C1207 " pdb=" CG PRO C1207 " model vdw 2.213 2.816 ... (remaining 56633 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 'A' and (resid 770 through 779 or (resid 780 through 782 and (name N or n \ ame CA or name C or name O or name CB )) or resid 783 through 838 or resid 987 t \ hrough 996 or (resid 997 through 998 and (name N or name CA or name C or name O \ or name CB )) or resid 999 through 1004 or (resid 1005 and (name N or name CA or \ name C or name O or name CB )) or resid 1006 through 1032 or (resid 1033 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1034 through 1050 or \ (resid 1051 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 052 through 1053 or (resid 1054 and (name N or name CA or name C or name O or na \ me CB )) or resid 1055 through 1066 or (resid 1067 through 1069 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1070 through 1104 or (resid 11 \ 05 and (name N or name CA or name C or name O or name CB )) or resid 1106 throug \ h 1120 or (resid 1121 and (name N or name CA or name C or name O or name CB )) o \ r resid 1122 through 1201 or (resid 1202 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1203 through 1204 or (resid 1205 through 1206 and (na \ me N or name CA or name C or name O or name CB )) or resid 1207 through 1257 or \ (resid 1258 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 59 through 1268 or (resid 1269 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1270 through 1271 or (resid 1272 through 1273 and (name N or na \ me CA or name C or name O or name CB )) or resid 1274 through 1305)) selection = (chain 'B' and ((resid 770 and (name N or name CA or name C or name O or name CB \ )) or resid 771 through 798 or (resid 799 and (name N or name CA or name C or n \ ame O or name CB )) or resid 800 through 838 or resid 987 through 996 or (resid \ 997 through 998 and (name N or name CA or name C or name O or name CB )) or resi \ d 999 through 1004 or (resid 1005 and (name N or name CA or name C or name O or \ name CB )) or resid 1006 through 1009 or (resid 1010 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1011 through 1050 or (resid 1051 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1052 through 1066 or ( \ resid 1067 through 1069 and (name N or name CA or name C or name O or name CB )) \ or resid 1070 through 1104 or (resid 1105 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1106 through 1112 or (resid 1113 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1114 through 1120 or (resid 1121 \ and (name N or name CA or name C or name O or name CB )) or resid 1122 through \ 1201 or (resid 1202 and (name N or name CA or name C or name O or name CB )) or \ resid 1203 through 1204 or (resid 1205 through 1206 and (name N or name CA or na \ me C or name O or name CB )) or resid 1207 through 1271 or (resid 1272 through 1 \ 273 and (name N or name CA or name C or name O or name CB )) or resid 1274 throu \ gh 1305)) selection = (chain 'C' and ((resid 770 and (name N or name CA or name C or name O or name CB \ )) or resid 771 through 779 or (resid 780 through 782 and (name N or name CA or \ name C or name O or name CB )) or resid 783 through 1009 or (resid 1010 and (na \ me N or name CA or name C or name O or name CB )) or resid 1011 through 1032 or \ (resid 1033 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 34 through 1053 or (resid 1054 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1055 through 1067 or (resid 1068 through 1069 and (name N or na \ me CA or name C or name O or name CB )) or resid 1070 through 1257 or (resid 125 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 1259 through \ 1275 or (resid 1276 and (name N or name CA or name C or name O or name CB )) or \ resid 1277 through 1305)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.810 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.242 7621 Z= 1.021 Angle : 2.275 39.430 10307 Z= 1.690 Chirality : 0.149 0.563 1243 Planarity : 0.026 0.304 1316 Dihedral : 16.478 175.500 2822 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 2.37 % Allowed : 4.64 % Favored : 92.99 % Rotamer: Outliers : 3.53 % Allowed : 16.69 % Favored : 79.78 % Cbeta Deviations : 2.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.26), residues: 1055 helix: 3.47 (0.18), residues: 501 sheet: -0.34 (0.49), residues: 129 loop : -1.96 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C1074 TYR 0.027 0.002 TYR C1141 PHE 0.027 0.003 PHE A1136 TRP 0.005 0.001 TRP B1184 HIS 0.008 0.003 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.01380 ( 7593) covalent geometry : angle 2.22523 (10235) SS BOND : bond 0.04678 ( 12) SS BOND : angle 8.92778 ( 24) hydrogen bonds : bond 0.20853 ( 504) hydrogen bonds : angle 7.84758 ( 1545) link_NAG-ASN : bond 0.00948 ( 16) link_NAG-ASN : angle 3.97596 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: A residue: PRO 1219 >>> skipping Corrupt residue: chain: A residue: PRO 1221 >>> skipping Corrupt residue: chain: B residue: PRO 1207 >>> skipping Corrupt residue: chain: B residue: PRO 1219 >>> skipping Corrupt residue: chain: B residue: PRO 1221 >>> skipping revert: symmetry clash Corrupt residue: chain: C residue: PRO 1207 >>> skipping Corrupt residue: chain: C residue: PRO 1219 >>> skipping Corrupt residue: chain: C residue: PRO 1221 >>> skipping REVERT: B 824 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.7029 (t80) REVERT: B 1029 ASN cc_start: 0.8270 (t0) cc_final: 0.7840 (t0) REVERT: B 1191 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: C 1191 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8596 (m-80) REVERT: C 1197 ILE cc_start: 0.9362 (mt) cc_final: 0.8935 (mt) outliers start: 28 outliers final: 16 residues processed: 180 average time/residue: 0.0403 time to fit residues: 11.2734 Evaluate side-chains 140 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1163 ASN Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1219 PRO Chi-restraints excluded: chain A residue 1221 PRO Chi-restraints excluded: chain B residue 824 TYR Chi-restraints excluded: chain B residue 1126 PHE Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1156 CYS Chi-restraints excluded: chain B residue 1163 ASN Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1191 PHE Chi-restraints excluded: chain B residue 1219 PRO Chi-restraints excluded: chain B residue 1221 PRO Chi-restraints excluded: chain B residue 1277 ASN Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1191 PHE Chi-restraints excluded: chain C residue 1219 PRO Chi-restraints excluded: chain C residue 1221 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN B 774 ASN B1160 ASN B1217 ASN ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.163869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.142852 restraints weight = 16698.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.142070 restraints weight = 24021.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.142728 restraints weight = 22545.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.142692 restraints weight = 16837.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.142918 restraints weight = 15892.060| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7621 Z= 0.175 Angle : 0.758 10.182 10307 Z= 0.388 Chirality : 0.049 0.364 1243 Planarity : 0.004 0.053 1316 Dihedral : 10.123 122.486 1455 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.83 % Favored : 94.69 % Rotamer: Outliers : 4.49 % Allowed : 19.42 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1055 helix: 2.98 (0.20), residues: 497 sheet: -0.76 (0.43), residues: 156 loop : -2.40 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1088 TYR 0.013 0.001 TYR B1141 PHE 0.016 0.002 PHE C 827 TRP 0.016 0.002 TRP A1184 HIS 0.010 0.003 HIS B1122 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7593) covalent geometry : angle 0.72344 (10235) SS BOND : bond 0.00886 ( 12) SS BOND : angle 2.42282 ( 24) hydrogen bonds : bond 0.06043 ( 504) hydrogen bonds : angle 5.09584 ( 1545) link_NAG-ASN : bond 0.00707 ( 16) link_NAG-ASN : angle 2.97373 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.278 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 1207 >>> skipping Corrupt residue: chain: A residue: PRO 1219 >>> skipping Corrupt residue: chain: A residue: PRO 1221 >>> skipping Corrupt residue: chain: B residue: PRO 1207 >>> skipping Corrupt residue: chain: B residue: PRO 1219 >>> skipping Corrupt residue: chain: B residue: PRO 1221 >>> skipping revert: symmetry clash Corrupt residue: chain: C residue: PRO 1207 >>> skipping Corrupt residue: chain: C residue: PRO 1219 >>> skipping Corrupt residue: chain: C residue: PRO 1221 >>> skipping REVERT: A 1116 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7771 (t80) REVERT: A 1184 TRP cc_start: 0.8406 (m100) cc_final: 0.8196 (m100) REVERT: B 824 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.6781 (t80) REVERT: B 1068 ASP cc_start: 0.7219 (t70) cc_final: 0.7015 (t0) REVERT: B 1191 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8415 (m-80) REVERT: C 786 PHE cc_start: 0.8366 (m-80) cc_final: 0.8137 (m-10) REVERT: C 1191 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: C 1235 LEU cc_start: 0.8150 (tp) cc_final: 0.7944 (tp) REVERT: C 1238 PHE cc_start: 0.7855 (p90) cc_final: 0.7609 (p90) outliers start: 34 outliers final: 19 residues processed: 173 average time/residue: 0.0404 time to fit residues: 11.1842 Evaluate side-chains 156 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 828 CYS Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1163 ASN Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1219 PRO Chi-restraints excluded: chain A residue 1221 PRO Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain B residue 824 TYR Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1191 PHE Chi-restraints excluded: chain B residue 1219 PRO Chi-restraints excluded: chain B residue 1221 PRO Chi-restraints excluded: chain B residue 1277 ASN Chi-restraints excluded: chain C residue 833 GLN Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1163 ASN Chi-restraints excluded: chain C residue 1164 CYS Chi-restraints excluded: chain C residue 1191 PHE Chi-restraints excluded: chain C residue 1219 PRO Chi-restraints excluded: chain C residue 1221 PRO Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 44 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 overall best weight: 1.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1029 ASN A1066 GLN B1009 GLN B1029 ASN C1029 ASN ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.159575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.138037 restraints weight = 16739.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.136825 restraints weight = 24933.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.137496 restraints weight = 22321.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.137394 restraints weight = 17823.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.137453 restraints weight = 16564.390| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7621 Z= 0.207 Angle : 0.709 16.952 10307 Z= 0.372 Chirality : 0.048 0.426 1243 Planarity : 0.004 0.057 1316 Dihedral : 9.187 125.756 1446 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.78 % Favored : 93.84 % Rotamer: Outliers : 6.10 % Allowed : 20.71 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 1055 helix: 2.70 (0.20), residues: 499 sheet: -0.99 (0.42), residues: 154 loop : -2.68 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1074 TYR 0.012 0.001 TYR B1141 PHE 0.020 0.002 PHE B1136 TRP 0.007 0.001 TRP A1184 HIS 0.009 0.003 HIS C1122 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 7593) covalent geometry : angle 0.66493 (10235) SS BOND : bond 0.00939 ( 12) SS BOND : angle 2.09958 ( 24) hydrogen bonds : bond 0.05422 ( 504) hydrogen bonds : angle 4.85965 ( 1545) link_NAG-ASN : bond 0.00660 ( 16) link_NAG-ASN : angle 3.38060 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.266 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 1207 >>> skipping Corrupt residue: chain: A residue: PRO 1219 >>> skipping Corrupt residue: chain: A residue: PRO 1221 >>> skipping Corrupt residue: chain: B residue: PRO 1207 >>> skipping Corrupt residue: chain: B residue: PRO 1219 >>> skipping Corrupt residue: chain: B residue: PRO 1221 >>> skipping Corrupt residue: chain: C residue: PRO 1207 >>> skipping Corrupt residue: chain: C residue: PRO 1219 >>> skipping Corrupt residue: chain: C residue: PRO 1221 >>> skipping REVERT: A 1184 TRP cc_start: 0.8544 (m100) cc_final: 0.8203 (m100) REVERT: B 1053 ASP cc_start: 0.7287 (p0) cc_final: 0.6909 (p0) REVERT: B 1068 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6907 (t0) REVERT: B 1191 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: C 1157 ASP cc_start: 0.6193 (OUTLIER) cc_final: 0.5724 (m-30) REVERT: C 1191 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8199 (m-80) outliers start: 44 outliers final: 27 residues processed: 148 average time/residue: 0.0419 time to fit residues: 9.9169 Evaluate side-chains 143 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1163 ASN Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1217 ASN Chi-restraints excluded: chain A residue 1219 PRO Chi-restraints excluded: chain A residue 1221 PRO Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1191 PHE Chi-restraints excluded: chain B residue 1219 PRO Chi-restraints excluded: chain B residue 1221 PRO Chi-restraints excluded: chain B residue 1240 LYS Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 824 TYR Chi-restraints excluded: chain C residue 1029 ASN Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1157 ASP Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1163 ASN Chi-restraints excluded: chain C residue 1191 PHE Chi-restraints excluded: chain C residue 1219 PRO Chi-restraints excluded: chain C residue 1221 PRO Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 67 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 ASN A1066 GLN B1029 ASN ** B1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1029 ASN ** C1138 HIS ** 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 = 0.4201 r_free = 0.4201 target = 0.152623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.128856 restraints weight = 16393.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.127395 restraints weight = 24222.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.129061 restraints weight = 19959.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.129164 restraints weight = 14010.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.129277 restraints weight = 12681.817| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7621 Z= 0.150 Angle : 0.697 19.337 10307 Z= 0.346 Chirality : 0.050 0.665 1243 Planarity : 0.004 0.049 1316 Dihedral : 8.710 121.714 1442 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.88 % Favored : 93.84 % Rotamer: Outliers : 4.65 % Allowed : 21.51 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 1055 helix: 2.86 (0.21), residues: 500 sheet: -1.05 (0.42), residues: 156 loop : -2.50 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C1074 TYR 0.013 0.001 TYR B1141 PHE 0.012 0.002 PHE C 827 TRP 0.008 0.001 TRP B1184 HIS 0.009 0.003 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7593) covalent geometry : angle 0.61211 (10235) SS BOND : bond 0.00758 ( 12) SS BOND : angle 1.77981 ( 24) hydrogen bonds : bond 0.04876 ( 504) hydrogen bonds : angle 4.55838 ( 1545) link_NAG-ASN : bond 0.01071 ( 16) link_NAG-ASN : angle 4.76965 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.249 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 1207 >>> skipping Corrupt residue: chain: A residue: PRO 1219 >>> skipping Corrupt residue: chain: A residue: PRO 1221 >>> skipping revert: symmetry clash Corrupt residue: chain: B residue: PRO 1207 >>> skipping Corrupt residue: chain: B residue: PRO 1219 >>> skipping Corrupt residue: chain: B residue: PRO 1221 >>> skipping revert: symmetry clash Corrupt residue: chain: C residue: PRO 1207 >>> skipping Corrupt residue: chain: C residue: PRO 1219 >>> skipping Corrupt residue: chain: C residue: PRO 1221 >>> skipping REVERT: A 1116 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7750 (t80) REVERT: B 1053 ASP cc_start: 0.7605 (p0) cc_final: 0.7277 (p0) REVERT: B 1191 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: C 1053 ASP cc_start: 0.7687 (p0) cc_final: 0.7359 (p0) REVERT: C 1068 ASP cc_start: 0.7184 (t70) cc_final: 0.6876 (t0) REVERT: C 1075 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8830 (mp) REVERT: C 1191 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.7942 (m-80) outliers start: 35 outliers final: 25 residues processed: 149 average time/residue: 0.0406 time to fit residues: 9.8435 Evaluate side-chains 152 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1219 PRO Chi-restraints excluded: chain A residue 1221 PRO Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1191 PHE Chi-restraints excluded: chain B residue 1219 PRO Chi-restraints excluded: chain B residue 1221 PRO Chi-restraints excluded: chain B residue 1240 LYS Chi-restraints excluded: chain B residue 1277 ASN Chi-restraints excluded: chain C residue 833 GLN Chi-restraints excluded: chain C residue 1028 ASN Chi-restraints excluded: chain C residue 1029 ASN Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1163 ASN Chi-restraints excluded: chain C residue 1191 PHE Chi-restraints excluded: chain C residue 1219 PRO Chi-restraints excluded: chain C residue 1221 PRO Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 33 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN B 772 GLN ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.159997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.139061 restraints weight = 16831.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.138184 restraints weight = 27295.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.138569 restraints weight = 25915.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.138326 restraints weight = 20685.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.138480 restraints weight = 18206.760| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7621 Z= 0.185 Angle : 0.711 19.174 10307 Z= 0.356 Chirality : 0.050 0.645 1243 Planarity : 0.004 0.045 1316 Dihedral : 8.583 122.065 1440 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.07 % Favored : 93.65 % Rotamer: Outliers : 5.46 % Allowed : 21.51 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1055 helix: 2.86 (0.21), residues: 500 sheet: -1.10 (0.42), residues: 154 loop : -2.65 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1074 TYR 0.013 0.001 TYR B1141 PHE 0.014 0.002 PHE B1136 TRP 0.022 0.002 TRP A1184 HIS 0.007 0.002 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7593) covalent geometry : angle 0.62842 (10235) SS BOND : bond 0.00759 ( 12) SS BOND : angle 1.82897 ( 24) hydrogen bonds : bond 0.04825 ( 504) hydrogen bonds : angle 4.55886 ( 1545) link_NAG-ASN : bond 0.01117 ( 16) link_NAG-ASN : angle 4.74785 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: A residue: PRO 1207 >>> skipping Corrupt residue: chain: A residue: PRO 1219 >>> skipping Corrupt residue: chain: A residue: PRO 1221 >>> skipping revert: symmetry clash Corrupt residue: chain: B residue: PRO 1207 >>> skipping Corrupt residue: chain: B residue: PRO 1219 >>> skipping Corrupt residue: chain: B residue: PRO 1221 >>> skipping revert: symmetry clash Corrupt residue: chain: C residue: PRO 1219 >>> skipping Corrupt residue: chain: C residue: PRO 1221 >>> skipping REVERT: A 1116 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7598 (t80) REVERT: B 1053 ASP cc_start: 0.7426 (p0) cc_final: 0.7038 (p0) REVERT: B 1126 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: B 1191 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: C 1053 ASP cc_start: 0.7266 (p0) cc_final: 0.6894 (p0) REVERT: C 1157 ASP cc_start: 0.5361 (OUTLIER) cc_final: 0.4786 (m-30) REVERT: C 1191 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.7891 (m-80) outliers start: 40 outliers final: 29 residues processed: 145 average time/residue: 0.0418 time to fit residues: 9.6560 Evaluate side-chains 144 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1219 PRO Chi-restraints excluded: chain A residue 1221 PRO Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1126 PHE Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1191 PHE Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain B residue 1219 PRO Chi-restraints excluded: chain B residue 1221 PRO Chi-restraints excluded: chain B residue 1277 ASN Chi-restraints excluded: chain C residue 833 GLN Chi-restraints excluded: chain C residue 1028 ASN Chi-restraints excluded: chain C residue 1029 ASN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1157 ASP Chi-restraints excluded: chain C residue 1163 ASN Chi-restraints excluded: chain C residue 1191 PHE Chi-restraints excluded: chain C residue 1201 ASN Chi-restraints excluded: chain C residue 1219 PRO Chi-restraints excluded: chain C residue 1221 PRO Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 ASN A1066 GLN B 772 GLN B1029 ASN C1023 GLN C1029 ASN ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.141079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111769 restraints weight = 15079.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.112700 restraints weight = 11576.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.113492 restraints weight = 9645.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.114175 restraints weight = 8371.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.114513 restraints weight = 7589.035| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7621 Z= 0.229 Angle : 0.748 19.133 10307 Z= 0.380 Chirality : 0.050 0.565 1243 Planarity : 0.004 0.048 1316 Dihedral : 8.833 125.815 1440 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.01 % Favored : 92.70 % Rotamer: Outliers : 5.62 % Allowed : 22.63 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.26), residues: 1055 helix: 2.74 (0.21), residues: 500 sheet: -1.19 (0.47), residues: 114 loop : -2.83 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A1074 TYR 0.011 0.001 TYR B1141 PHE 0.018 0.002 PHE B1136 TRP 0.020 0.003 TRP A1184 HIS 0.006 0.002 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 7593) covalent geometry : angle 0.67092 (10235) SS BOND : bond 0.00899 ( 12) SS BOND : angle 1.99615 ( 24) hydrogen bonds : bond 0.04981 ( 504) hydrogen bonds : angle 4.70406 ( 1545) link_NAG-ASN : bond 0.01083 ( 16) link_NAG-ASN : angle 4.71892 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.182 Fit side-chains Corrupt residue: chain: A residue: PRO 1207 >>> skipping Corrupt residue: chain: A residue: PRO 1219 >>> skipping Corrupt residue: chain: A residue: PRO 1221 >>> skipping revert: symmetry clash Corrupt residue: chain: B residue: PRO 1207 >>> skipping Corrupt residue: chain: B residue: PRO 1219 >>> skipping Corrupt residue: chain: B residue: PRO 1221 >>> skipping revert: symmetry clash Corrupt residue: chain: C residue: PRO 1219 >>> skipping Corrupt residue: chain: C residue: PRO 1221 >>> skipping REVERT: A 1116 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7568 (t80) REVERT: B 1053 ASP cc_start: 0.8080 (p0) cc_final: 0.7845 (p0) REVERT: B 1126 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: C 1157 ASP cc_start: 0.5654 (OUTLIER) cc_final: 0.5387 (m-30) outliers start: 41 outliers final: 32 residues processed: 142 average time/residue: 0.0429 time to fit residues: 9.8788 Evaluate side-chains 134 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1219 PRO Chi-restraints excluded: chain A residue 1221 PRO Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1126 PHE Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1191 PHE Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain B residue 1219 PRO Chi-restraints excluded: chain B residue 1221 PRO Chi-restraints excluded: chain B residue 1277 ASN Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 833 GLN Chi-restraints excluded: chain C residue 1028 ASN Chi-restraints excluded: chain C residue 1029 ASN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1157 ASP Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain C residue 1219 PRO Chi-restraints excluded: chain C residue 1221 PRO Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.143187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.116979 restraints weight = 15222.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115649 restraints weight = 18662.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.116571 restraints weight = 17184.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.116851 restraints weight = 14418.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117179 restraints weight = 12227.509| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7621 Z= 0.158 Angle : 0.688 18.968 10307 Z= 0.345 Chirality : 0.048 0.543 1243 Planarity : 0.004 0.049 1316 Dihedral : 8.317 121.425 1436 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.59 % Favored : 94.12 % Rotamer: Outliers : 4.65 % Allowed : 24.08 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 1055 helix: 2.97 (0.21), residues: 502 sheet: -1.26 (0.44), residues: 134 loop : -2.68 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1088 TYR 0.013 0.001 TYR B1141 PHE 0.016 0.002 PHE C1231 TRP 0.032 0.004 TRP A1184 HIS 0.006 0.002 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7593) covalent geometry : angle 0.61000 (10235) SS BOND : bond 0.00699 ( 12) SS BOND : angle 1.53396 ( 24) hydrogen bonds : bond 0.04611 ( 504) hydrogen bonds : angle 4.55145 ( 1545) link_NAG-ASN : bond 0.01060 ( 16) link_NAG-ASN : angle 4.58747 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.213 Fit side-chains Corrupt residue: chain: A residue: PRO 1207 >>> skipping Corrupt residue: chain: A residue: PRO 1219 >>> skipping Corrupt residue: chain: A residue: PRO 1221 >>> skipping revert: symmetry clash Corrupt residue: chain: B residue: PRO 1207 >>> skipping Corrupt residue: chain: B residue: PRO 1219 >>> skipping Corrupt residue: chain: B residue: PRO 1221 >>> skipping revert: symmetry clash Corrupt residue: chain: C residue: PRO 1219 >>> skipping Corrupt residue: chain: C residue: PRO 1221 >>> skipping REVERT: A 1116 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7687 (t80) REVERT: B 1053 ASP cc_start: 0.7941 (p0) cc_final: 0.7717 (p0) REVERT: B 1126 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8268 (m-80) outliers start: 35 outliers final: 30 residues processed: 134 average time/residue: 0.0373 time to fit residues: 8.1355 Evaluate side-chains 130 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1219 PRO Chi-restraints excluded: chain A residue 1221 PRO Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1126 PHE Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1191 PHE Chi-restraints excluded: chain B residue 1219 PRO Chi-restraints excluded: chain B residue 1221 PRO Chi-restraints excluded: chain B residue 1277 ASN Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 833 GLN Chi-restraints excluded: chain C residue 1028 ASN Chi-restraints excluded: chain C residue 1029 ASN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain C residue 1219 PRO Chi-restraints excluded: chain C residue 1221 PRO Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.0070 chunk 3 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 772 GLN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 ASN A1066 GLN B 772 GLN B1029 ASN C1029 ASN ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.145615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.120216 restraints weight = 14806.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118885 restraints weight = 18508.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119980 restraints weight = 17817.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.120095 restraints weight = 13996.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.120306 restraints weight = 13697.511| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7621 Z= 0.143 Angle : 0.666 18.689 10307 Z= 0.332 Chirality : 0.047 0.488 1243 Planarity : 0.004 0.051 1316 Dihedral : 7.991 116.980 1436 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.69 % Favored : 94.03 % Rotamer: Outliers : 4.17 % Allowed : 24.72 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.27), residues: 1055 helix: 3.09 (0.21), residues: 508 sheet: -1.27 (0.44), residues: 134 loop : -2.51 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1088 TYR 0.013 0.001 TYR B1141 PHE 0.015 0.001 PHE C1231 TRP 0.026 0.004 TRP A1184 HIS 0.006 0.002 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7593) covalent geometry : angle 0.59096 (10235) SS BOND : bond 0.00548 ( 12) SS BOND : angle 1.28184 ( 24) hydrogen bonds : bond 0.04336 ( 504) hydrogen bonds : angle 4.46168 ( 1545) link_NAG-ASN : bond 0.01018 ( 16) link_NAG-ASN : angle 4.46750 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.283 Fit side-chains revert: symmetry clash Corrupt residue: chain: A residue: PRO 1207 >>> skipping Corrupt residue: chain: A residue: PRO 1219 >>> skipping Corrupt residue: chain: A residue: PRO 1221 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 1207 >>> skipping Corrupt residue: chain: B residue: PRO 1219 >>> skipping Corrupt residue: chain: B residue: PRO 1221 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: C residue: PRO 1219 >>> skipping Corrupt residue: chain: C residue: PRO 1221 >>> skipping REVERT: A 1116 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7714 (t80) REVERT: C 1053 ASP cc_start: 0.8018 (p0) cc_final: 0.7737 (p0) outliers start: 32 outliers final: 30 residues processed: 132 average time/residue: 0.0435 time to fit residues: 9.3631 Evaluate side-chains 133 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1219 PRO Chi-restraints excluded: chain A residue 1221 PRO Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1219 PRO Chi-restraints excluded: chain B residue 1221 PRO Chi-restraints excluded: chain B residue 1277 ASN Chi-restraints excluded: chain C residue 833 GLN Chi-restraints excluded: chain C residue 1029 ASN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1157 ASP Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain C residue 1219 PRO Chi-restraints excluded: chain C residue 1221 PRO Chi-restraints excluded: chain C residue 1235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 11 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 772 GLN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 GLN B1066 GLN ** C1138 HIS ** 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 = 0.3989 r_free = 0.3989 target = 0.140435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.114430 restraints weight = 15205.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.112089 restraints weight = 12073.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.112090 restraints weight = 12855.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.112085 restraints weight = 12972.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.112230 restraints weight = 11765.707| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7621 Z= 0.287 Angle : 0.789 18.445 10307 Z= 0.405 Chirality : 0.050 0.468 1243 Planarity : 0.004 0.048 1316 Dihedral : 8.458 125.524 1434 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.49 % Favored : 92.23 % Rotamer: Outliers : 4.98 % Allowed : 24.56 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.26), residues: 1055 helix: 2.65 (0.21), residues: 509 sheet: -1.58 (0.46), residues: 114 loop : -2.81 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1074 TYR 0.010 0.001 TYR B1141 PHE 0.019 0.002 PHE B1136 TRP 0.030 0.004 TRP A1184 HIS 0.003 0.002 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00638 ( 7593) covalent geometry : angle 0.72213 (10235) SS BOND : bond 0.00905 ( 12) SS BOND : angle 1.83248 ( 24) hydrogen bonds : bond 0.05035 ( 504) hydrogen bonds : angle 4.81119 ( 1545) link_NAG-ASN : bond 0.01070 ( 16) link_NAG-ASN : angle 4.54944 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.180 Fit side-chains Corrupt residue: chain: A residue: PRO 1207 >>> skipping Corrupt residue: chain: A residue: PRO 1219 >>> skipping Corrupt residue: chain: A residue: PRO 1221 >>> skipping revert: symmetry clash Corrupt residue: chain: B residue: PRO 1207 >>> skipping Corrupt residue: chain: B residue: PRO 1219 >>> skipping Corrupt residue: chain: B residue: PRO 1221 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: C residue: PRO 1219 >>> skipping Corrupt residue: chain: C residue: PRO 1221 >>> skipping REVERT: A 1116 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7615 (t80) REVERT: B 1126 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8394 (m-80) outliers start: 37 outliers final: 34 residues processed: 121 average time/residue: 0.0412 time to fit residues: 8.1359 Evaluate side-chains 121 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1219 PRO Chi-restraints excluded: chain A residue 1221 PRO Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1126 PHE Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1205 VAL Chi-restraints excluded: chain B residue 1219 PRO Chi-restraints excluded: chain B residue 1221 PRO Chi-restraints excluded: chain B residue 1277 ASN Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 833 GLN Chi-restraints excluded: chain C residue 1028 ASN Chi-restraints excluded: chain C residue 1029 ASN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain C residue 1219 PRO Chi-restraints excluded: chain C residue 1221 PRO Chi-restraints excluded: chain C residue 1235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 ASN B1029 ASN C1029 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.144890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.119305 restraints weight = 14758.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.117725 restraints weight = 18780.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.118895 restraints weight = 17643.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.118988 restraints weight = 12926.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.119120 restraints weight = 11636.591| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7621 Z= 0.145 Angle : 0.689 18.496 10307 Z= 0.345 Chirality : 0.047 0.456 1243 Planarity : 0.004 0.049 1316 Dihedral : 8.067 118.965 1434 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.50 % Favored : 94.22 % Rotamer: Outliers : 3.69 % Allowed : 25.84 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.27), residues: 1055 helix: 3.03 (0.21), residues: 508 sheet: -1.48 (0.44), residues: 134 loop : -2.56 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1088 TYR 0.014 0.001 TYR B1141 PHE 0.014 0.001 PHE C1231 TRP 0.023 0.003 TRP A1184 HIS 0.007 0.002 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7593) covalent geometry : angle 0.61862 (10235) SS BOND : bond 0.00585 ( 12) SS BOND : angle 1.26712 ( 24) hydrogen bonds : bond 0.04413 ( 504) hydrogen bonds : angle 4.55130 ( 1545) link_NAG-ASN : bond 0.01007 ( 16) link_NAG-ASN : angle 4.41488 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.262 Fit side-chains Corrupt residue: chain: A residue: PRO 1207 >>> skipping Corrupt residue: chain: A residue: PRO 1219 >>> skipping Corrupt residue: chain: A residue: PRO 1221 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 1207 >>> skipping Corrupt residue: chain: B residue: PRO 1219 >>> skipping Corrupt residue: chain: B residue: PRO 1221 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: C residue: PRO 1219 >>> skipping Corrupt residue: chain: C residue: PRO 1221 >>> skipping REVERT: A 1116 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7757 (t80) outliers start: 29 outliers final: 28 residues processed: 126 average time/residue: 0.0427 time to fit residues: 8.8483 Evaluate side-chains 130 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1219 PRO Chi-restraints excluded: chain A residue 1221 PRO Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1164 CYS Chi-restraints excluded: chain B residue 1219 PRO Chi-restraints excluded: chain B residue 1221 PRO Chi-restraints excluded: chain B residue 1277 ASN Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain C residue 833 GLN Chi-restraints excluded: chain C residue 1029 ASN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1157 ASP Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain C residue 1219 PRO Chi-restraints excluded: chain C residue 1221 PRO Chi-restraints excluded: chain C residue 1235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 60 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 772 GLN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 GLN B1029 ASN C1029 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.144226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118640 restraints weight = 14733.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116733 restraints weight = 21028.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.117976 restraints weight = 20862.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.118510 restraints weight = 14741.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.118385 restraints weight = 13921.541| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7621 Z= 0.171 Angle : 0.693 18.312 10307 Z= 0.348 Chirality : 0.047 0.435 1243 Planarity : 0.004 0.049 1316 Dihedral : 8.067 119.432 1434 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.16 % Favored : 93.55 % Rotamer: Outliers : 4.49 % Allowed : 25.36 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 1055 helix: 2.87 (0.21), residues: 517 sheet: -1.51 (0.43), residues: 134 loop : -2.65 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1074 TYR 0.013 0.001 TYR B1141 PHE 0.013 0.002 PHE B1136 TRP 0.022 0.003 TRP A1184 HIS 0.006 0.002 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7593) covalent geometry : angle 0.62315 (10235) SS BOND : bond 0.00624 ( 12) SS BOND : angle 1.35259 ( 24) hydrogen bonds : bond 0.04469 ( 504) hydrogen bonds : angle 4.58336 ( 1545) link_NAG-ASN : bond 0.01000 ( 16) link_NAG-ASN : angle 4.39237 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1020.24 seconds wall clock time: 18 minutes 16.61 seconds (1096.61 seconds total)