Starting phenix.real_space_refine on Fri Sep 11 06:27:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6m3w_30072/09_2026/6m3w_30072.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m3w_30072/09_2026/6m3w_30072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m3w_30072/09_2026/6m3w_30072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m3w_30072/09_2026/6m3w_30072.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6m3w_30072/09_2026/6m3w_30072.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6m3w_30072/09_2026/6m3w_30072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m3w_30072/09_2026/6m3w_30072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m3w_30072/09_2026/6m3w_30072.map" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.003 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 39 5.16 5 C 5190 2.51 5 N 1386 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8307 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2657 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 11, 'TRANS': 332} Chain breaks: 1 Chain: "B" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2657 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 11, 'TRANS': 332} Chain breaks: 1 Chain: "C" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2657 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 11, 'TRANS': 332} Chain breaks: 1 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 1.93, per 1000 atoms: 0.23 Number of scatterers: 8307 At special positions: 0 Unit cell: (73, 73, 208, 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 39 16.00 O 1692 8.00 N 1386 7.00 C 5190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.02 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.02 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.02 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.02 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1201 " - " ASN A1176 " " NAG A1202 " - " ASN A1155 " " NAG A1203 " - " ASN A1140 " " NAG A1204 " - " ASN A1116 " " NAG A1205 " - " ASN A1080 " " NAG A1206 " - " ASN A1056 " " NAG A1207 " - " ASN A 699 " " NAG A1208 " - " ASN A 691 " " NAG B1201 " - " ASN B1176 " " NAG B1202 " - " ASN B1155 " " NAG B1203 " - " ASN B1140 " " NAG B1204 " - " ASN B1116 " " NAG B1205 " - " ASN B1080 " " NAG B1206 " - " ASN B1056 " " NAG B1207 " - " ASN B 699 " " NAG B1208 " - " ASN B 691 " " NAG C1201 " - " ASN C1176 " " NAG C1202 " - " ASN C1155 " " NAG C1203 " - " ASN C1140 " " NAG C1204 " - " ASN C1116 " " NAG C1205 " - " ASN C1080 " " NAG C1206 " - " ASN C1056 " " NAG C1207 " - " ASN C 699 " " NAG C1208 " - " ASN C 691 " Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 424.0 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1962 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 12 sheets defined 50.6% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.781A pdb=" N ALA A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 753 removed outlier: 3.559A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 1014 removed outlier: 3.629A pdb=" N ALA A 906 " --> pdb=" O GLN A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1137 removed outlier: 3.779A pdb=" N TYR A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1154 removed outlier: 3.588A pdb=" N ILE A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1178 removed outlier: 3.525A pdb=" N SER A1178 " --> pdb=" O ASN A1174 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.781A pdb=" N ALA B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 753 removed outlier: 3.558A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 1014 removed outlier: 3.629A pdb=" N ALA B 906 " --> pdb=" O GLN B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1137 removed outlier: 3.779A pdb=" N TYR B1137 " --> pdb=" O GLU B1133 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1154 removed outlier: 3.588A pdb=" N ILE B1154 " --> pdb=" O ASP B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1178 removed outlier: 3.526A pdb=" N SER B1178 " --> pdb=" O ASN B1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 728 through 736 removed outlier: 3.782A pdb=" N ALA C 732 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 753 removed outlier: 3.559A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 1014 removed outlier: 3.630A pdb=" N ALA C 906 " --> pdb=" O GLN C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1137 removed outlier: 3.779A pdb=" N TYR C1137 " --> pdb=" O GLU C1133 " (cutoff:3.500A) Processing helix chain 'C' and resid 1149 through 1154 removed outlier: 3.589A pdb=" N ILE C1154 " --> pdb=" O ASP C1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 1162 through 1178 removed outlier: 3.526A pdb=" N SER C1178 " --> pdb=" O ASN C1174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 692 through 704 removed outlier: 3.575A pdb=" N ARG A1055 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN A1053 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE A 700 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 702 " --> pdb=" O TYR A1049 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR A1049 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE A 704 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL A1047 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 709 " --> pdb=" O VAL A1042 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 692 through 704 removed outlier: 3.575A pdb=" N ARG A1055 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN A1053 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE A 700 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 702 " --> pdb=" O TYR A1049 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR A1049 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE A 704 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL A1047 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1071 through 1072 Processing sheet with id=AA4, first strand: chain 'A' and resid 1077 through 1078 Processing sheet with id=AA5, first strand: chain 'B' and resid 692 through 704 removed outlier: 3.575A pdb=" N ARG B1055 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET B 709 " --> pdb=" O VAL B1042 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 692 through 704 removed outlier: 3.575A pdb=" N ARG B1055 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1071 through 1072 Processing sheet with id=AA8, first strand: chain 'B' and resid 1077 through 1078 Processing sheet with id=AA9, first strand: chain 'C' and resid 692 through 704 removed outlier: 3.575A pdb=" N ARG C1055 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN C1053 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE C 700 " --> pdb=" O PRO C1051 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 702 " --> pdb=" O TYR C1049 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR C1049 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE C 704 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C1047 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET C 709 " --> pdb=" O VAL C1042 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 692 through 704 removed outlier: 3.575A pdb=" N ARG C1055 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN C1053 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE C 700 " --> pdb=" O PRO C1051 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 702 " --> pdb=" O TYR C1049 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR C1049 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE C 704 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C1047 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1071 through 1072 Processing sheet with id=AB3, first strand: chain 'C' and resid 1077 through 1078 489 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2584 1.34 - 1.46: 1565 1.46 - 1.57: 4227 1.57 - 1.69: 3 1.69 - 1.81: 54 Bond restraints: 8433 Sorted by residual: bond pdb=" C1 NAG C1205 " pdb=" O5 NAG C1205 " ideal model delta sigma weight residual 1.406 1.518 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C1 NAG A1202 " pdb=" O5 NAG A1202 " ideal model delta sigma weight residual 1.406 1.516 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C1 NAG B1202 " pdb=" O5 NAG B1202 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C1 NAG B1205 " pdb=" O5 NAG B1205 " ideal model delta sigma weight residual 1.406 1.512 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C1 NAG A1205 " pdb=" O5 NAG A1205 " ideal model delta sigma weight residual 1.406 1.512 -0.106 2.00e-02 2.50e+03 2.79e+01 ... (remaining 8428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10494 2.10 - 4.20: 743 4.20 - 6.30: 178 6.30 - 8.40: 12 8.40 - 10.50: 21 Bond angle restraints: 11448 Sorted by residual: angle pdb=" N LEU C1148 " pdb=" CA LEU C1148 " pdb=" C LEU C1148 " ideal model delta sigma weight residual 111.02 116.69 -5.67 1.22e+00 6.72e-01 2.16e+01 angle pdb=" N LEU B1148 " pdb=" CA LEU B1148 " pdb=" C LEU B1148 " ideal model delta sigma weight residual 111.02 116.69 -5.67 1.22e+00 6.72e-01 2.16e+01 angle pdb=" N LEU A1148 " pdb=" CA LEU A1148 " pdb=" C LEU A1148 " ideal model delta sigma weight residual 111.02 116.66 -5.64 1.22e+00 6.72e-01 2.14e+01 angle pdb=" C ASP A1147 " pdb=" N LEU A1148 " pdb=" CA LEU A1148 " ideal model delta sigma weight residual 120.79 125.79 -5.00 1.39e+00 5.18e-01 1.30e+01 angle pdb=" C ASP B1147 " pdb=" N LEU B1148 " pdb=" CA LEU B1148 " ideal model delta sigma weight residual 120.79 125.79 -5.00 1.39e+00 5.18e-01 1.29e+01 ... (remaining 11443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 4602 16.34 - 32.68: 270 32.68 - 49.03: 60 49.03 - 65.37: 0 65.37 - 81.71: 9 Dihedral angle restraints: 4941 sinusoidal: 1926 harmonic: 3015 Sorted by residual: dihedral pdb=" CA GLN A1124 " pdb=" C GLN A1124 " pdb=" N PRO A1125 " pdb=" CA PRO A1125 " ideal model delta harmonic sigma weight residual 180.00 -134.26 -45.74 0 5.00e+00 4.00e-02 8.37e+01 dihedral pdb=" CA GLN B1124 " pdb=" C GLN B1124 " pdb=" N PRO B1125 " pdb=" CA PRO B1125 " ideal model delta harmonic sigma weight residual -180.00 -134.26 -45.74 0 5.00e+00 4.00e-02 8.37e+01 dihedral pdb=" CA GLN C1124 " pdb=" C GLN C1124 " pdb=" N PRO C1125 " pdb=" CA PRO C1125 " ideal model delta harmonic sigma weight residual -180.00 -134.31 -45.69 0 5.00e+00 4.00e-02 8.35e+01 ... (remaining 4938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1261 0.110 - 0.220: 140 0.220 - 0.331: 12 0.331 - 0.441: 1 0.441 - 0.551: 5 Chirality restraints: 1419 Sorted by residual: chirality pdb=" C1 NAG A1207 " pdb=" ND2 ASN A 699 " pdb=" C2 NAG A1207 " pdb=" O5 NAG A1207 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" C1 NAG C1207 " pdb=" ND2 ASN C 699 " pdb=" C2 NAG C1207 " pdb=" O5 NAG C1207 " 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=" C1 NAG B1207 " pdb=" ND2 ASN B 699 " pdb=" C2 NAG B1207 " pdb=" O5 NAG B1207 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.57e+00 ... (remaining 1416 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C1143 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.56e+00 pdb=" N PRO C1144 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C1144 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C1144 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B1143 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO B1144 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B1144 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B1144 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1143 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO A1144 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1144 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1144 " -0.040 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2120 2.79 - 3.32: 8589 3.32 - 3.85: 14709 3.85 - 4.37: 16295 4.37 - 4.90: 26427 Nonbonded interactions: 68140 Sorted by model distance: nonbonded pdb=" O GLY B1149 " pdb=" OG SER B1152 " model vdw 2.264 3.040 nonbonded pdb=" O GLY C1149 " pdb=" OG SER C1152 " model vdw 2.264 3.040 nonbonded pdb=" O GLY A1149 " pdb=" OG SER A1152 " model vdw 2.264 3.040 nonbonded pdb=" OD2 ASP A1145 " pdb=" OG SER C 956 " model vdw 2.286 3.040 nonbonded pdb=" O GLU B 918 " pdb=" OG1 THR B 922 " model vdw 2.293 3.040 ... (remaining 68135 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.730 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.011 0.112 8469 Z= 0.514 Angle : 1.369 14.712 11544 Z= 0.700 Chirality : 0.078 0.551 1419 Planarity : 0.009 0.073 1461 Dihedral : 11.586 74.819 2943 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 0.66 % Allowed : 2.99 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.60 % 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: -4.25 (0.20), residues: 1020 helix: -1.53 (0.18), residues: 498 sheet: -3.57 (0.43), residues: 99 loop : -4.27 (0.21), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B1055 TYR 0.023 0.004 TYR B1029 PHE 0.038 0.006 PHE C 952 TRP 0.016 0.006 TRP B1084 HIS 0.006 0.002 HIS B1030 Details of bonding type rmsd/Z covalent geometry : bond 0.01096 / 0.51 ( 8433) covalent geometry : angle 1.30693 / 0.69 (11448) SS BOND : bond 0.00741 / 0.44 ( 12) SS BOND : angle 2.03832 / 1.12 ( 24) hydrogen bonds : bond 0.13763 / 9.29 ( 471) hydrogen bonds : angle 7.83782 / 5.56 ( 1422) link_NAG-ASN : bond 0.01558 / 0.90 ( 24) link_NAG-ASN : angle 5.23566 / 3.65 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 227 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 907 ASN cc_start: 0.7897 (m-40) cc_final: 0.7552 (p0) REVERT: A 989 TYR cc_start: 0.8299 (t80) cc_final: 0.7810 (t80) REVERT: A 1070 TYR cc_start: 0.7321 (m-80) cc_final: 0.6847 (m-80) REVERT: B 907 ASN cc_start: 0.7895 (m-40) cc_final: 0.7577 (p0) REVERT: B 989 TYR cc_start: 0.8278 (t80) cc_final: 0.7906 (t80) REVERT: C 907 ASN cc_start: 0.7801 (m-40) cc_final: 0.7354 (p0) REVERT: C 976 ASP cc_start: 0.7539 (m-30) cc_final: 0.6591 (m-30) REVERT: C 994 LEU cc_start: 0.9438 (mt) cc_final: 0.9209 (tp) REVERT: C 1130 PHE cc_start: 0.8658 (m-80) cc_final: 0.8454 (m-80) outliers start: 6 outliers final: 0 residues processed: 233 average time/residue: 0.1002 time to fit residues: 30.8303 Evaluate side-chains 126 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN A1090 ASN A1141 HIS ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN B1065 HIS ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 ASN C 993 GLN C1090 ASN C1141 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.071940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062392 restraints weight = 37995.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.063992 restraints weight = 22894.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.065121 restraints weight = 15922.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065850 restraints weight = 12092.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.066458 restraints weight = 9887.089| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8469 Z= 0.175 Angle : 0.845 9.590 11544 Z= 0.406 Chirality : 0.061 0.398 1419 Planarity : 0.006 0.057 1461 Dihedral : 7.048 37.404 1086 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.77 % Allowed : 11.74 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.10 % 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: -2.63 (0.23), residues: 1020 helix: 0.08 (0.21), residues: 492 sheet: -3.17 (0.43), residues: 117 loop : -3.67 (0.23), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 996 TYR 0.015 0.001 TYR C 989 PHE 0.022 0.002 PHE B1079 TRP 0.004 0.001 TRP A1084 HIS 0.002 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 8433) covalent geometry : angle 0.80672 / 0.40 (11448) SS BOND : bond 0.00299 / 0.20 ( 12) SS BOND : angle 1.15225 / 0.66 ( 24) hydrogen bonds : bond 0.05156 / 3.44 ( 471) hydrogen bonds : angle 5.71243 / 4.09 ( 1422) link_NAG-ASN : bond 0.00858 / 0.50 ( 24) link_NAG-ASN : angle 3.23617 / 2.23 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 996 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7271 (tpt170) REVERT: B 1131 LYS cc_start: 0.8336 (mmpt) cc_final: 0.8017 (mmtm) REVERT: B 1166 ASP cc_start: 0.8018 (m-30) cc_final: 0.7668 (t0) REVERT: C 976 ASP cc_start: 0.7495 (m-30) cc_final: 0.7176 (m-30) REVERT: C 994 LEU cc_start: 0.9472 (mt) cc_final: 0.9270 (mt) REVERT: C 1166 ASP cc_start: 0.8038 (m-30) cc_final: 0.7782 (t0) outliers start: 34 outliers final: 14 residues processed: 186 average time/residue: 0.0872 time to fit residues: 22.1704 Evaluate side-chains 135 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1084 TRP Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 1019 SER Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1176 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN B1141 HIS ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.070656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.061091 restraints weight = 37898.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.062638 restraints weight = 23178.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.063742 restraints weight = 16231.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064474 restraints weight = 12356.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.065059 restraints weight = 10052.022| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8469 Z= 0.200 Angle : 0.821 9.462 11544 Z= 0.394 Chirality : 0.060 0.342 1419 Planarity : 0.005 0.047 1461 Dihedral : 6.614 35.641 1086 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.65 % Allowed : 13.18 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -2.15 (0.24), residues: 1020 helix: 0.67 (0.22), residues: 495 sheet: -3.13 (0.42), residues: 117 loop : -3.69 (0.24), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 977 TYR 0.011 0.002 TYR C 738 PHE 0.015 0.002 PHE B1079 TRP 0.003 0.001 TRP C1084 HIS 0.012 0.001 HIS B1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 ( 8433) covalent geometry : angle 0.78865 / 0.39 (11448) SS BOND : bond 0.00466 / 0.31 ( 12) SS BOND : angle 1.26749 / 0.76 ( 24) hydrogen bonds : bond 0.05125 / 3.38 ( 471) hydrogen bonds : angle 5.38293 / 3.86 ( 1422) link_NAG-ASN : bond 0.00790 / 0.47 ( 24) link_NAG-ASN : angle 2.91919 / 2.00 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 936 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 976 ASP cc_start: 0.7901 (m-30) cc_final: 0.6691 (m-30) REVERT: B 1130 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7983 (t80) REVERT: B 1166 ASP cc_start: 0.8056 (m-30) cc_final: 0.7815 (t0) REVERT: C 972 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: C 977 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8056 (mpt-90) REVERT: C 1130 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8026 (t80) outliers start: 42 outliers final: 24 residues processed: 150 average time/residue: 0.0871 time to fit residues: 18.1123 Evaluate side-chains 131 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1084 TRP Chi-restraints excluded: chain B residue 1130 PHE Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1130 PHE Chi-restraints excluded: chain C residue 1176 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 ASN A1174 ASN ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN ** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 ASN ** C 942 ASN ** 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 = 0.3520 r_free = 0.3520 target = 0.069631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059793 restraints weight = 39396.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061356 restraints weight = 24116.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.062440 restraints weight = 16904.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.063218 restraints weight = 12961.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.063669 restraints weight = 10556.167| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8469 Z= 0.241 Angle : 0.831 9.558 11544 Z= 0.403 Chirality : 0.060 0.341 1419 Planarity : 0.005 0.046 1461 Dihedral : 6.499 34.432 1086 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 5.54 % Allowed : 13.73 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -2.06 (0.25), residues: 1020 helix: 0.82 (0.22), residues: 492 sheet: -2.87 (0.37), residues: 141 loop : -3.80 (0.24), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 977 TYR 0.010 0.001 TYR B1120 PHE 0.018 0.002 PHE B1057 TRP 0.004 0.001 TRP C1084 HIS 0.004 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 ( 8433) covalent geometry : angle 0.80269 / 0.40 (11448) SS BOND : bond 0.00305 / 0.19 ( 12) SS BOND : angle 1.40578 / 0.85 ( 24) hydrogen bonds : bond 0.05321 / 3.51 ( 471) hydrogen bonds : angle 5.26662 / 3.80 ( 1422) link_NAG-ASN : bond 0.00766 / 0.46 ( 24) link_NAG-ASN : angle 2.76696 / 1.89 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1070 TYR cc_start: 0.7227 (m-80) cc_final: 0.6881 (m-80) REVERT: B 976 ASP cc_start: 0.7827 (m-30) cc_final: 0.7355 (m-30) REVERT: B 1020 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8701 (mtpp) REVERT: B 1130 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8154 (t80) REVERT: B 1166 ASP cc_start: 0.8037 (m-30) cc_final: 0.7799 (t0) REVERT: C 976 ASP cc_start: 0.7596 (m-30) cc_final: 0.6957 (m-30) REVERT: C 1130 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8068 (t80) outliers start: 50 outliers final: 35 residues processed: 136 average time/residue: 0.0828 time to fit residues: 15.5113 Evaluate side-chains 130 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1084 TRP Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1130 PHE Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1130 PHE Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1176 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 942 ASN ** 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 = 0.3515 r_free = 0.3515 target = 0.069549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.059573 restraints weight = 39031.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.061137 restraints weight = 23729.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.062251 restraints weight = 16646.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.062970 restraints weight = 12790.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.063523 restraints weight = 10566.164| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8469 Z= 0.218 Angle : 0.802 9.564 11544 Z= 0.388 Chirality : 0.059 0.349 1419 Planarity : 0.005 0.056 1461 Dihedral : 6.352 33.806 1086 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 4.98 % Allowed : 16.28 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % 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: -2.04 (0.24), residues: 1020 helix: 0.93 (0.22), residues: 495 sheet: -2.86 (0.38), residues: 132 loop : -3.97 (0.22), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 977 TYR 0.008 0.001 TYR B1120 PHE 0.016 0.002 PHE C1057 TRP 0.003 0.001 TRP B1084 HIS 0.004 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 ( 8433) covalent geometry : angle 0.77286 / 0.38 (11448) SS BOND : bond 0.00302 / 0.18 ( 12) SS BOND : angle 1.45044 / 0.88 ( 24) hydrogen bonds : bond 0.05121 / 3.37 ( 471) hydrogen bonds : angle 5.09700 / 3.68 ( 1422) link_NAG-ASN : bond 0.00753 / 0.45 ( 24) link_NAG-ASN : angle 2.71087 / 1.85 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 101 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1070 TYR cc_start: 0.7211 (m-80) cc_final: 0.6884 (m-80) REVERT: B 976 ASP cc_start: 0.7917 (m-30) cc_final: 0.7306 (m-30) REVERT: B 1166 ASP cc_start: 0.8035 (m-30) cc_final: 0.7796 (t0) REVERT: C 976 ASP cc_start: 0.7530 (m-30) cc_final: 0.6882 (m-30) REVERT: C 977 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8344 (mtt90) REVERT: C 1130 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8433 (t80) outliers start: 45 outliers final: 36 residues processed: 132 average time/residue: 0.0846 time to fit residues: 15.3393 Evaluate side-chains 129 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1084 TRP Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1130 PHE Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1176 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 26 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 0.0010 chunk 23 optimal weight: 0.0050 chunk 3 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.071161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.061199 restraints weight = 38710.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062797 restraints weight = 23826.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.063883 restraints weight = 16749.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.064662 restraints weight = 12922.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.065214 restraints weight = 10575.337| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8469 Z= 0.156 Angle : 0.750 9.473 11544 Z= 0.360 Chirality : 0.058 0.354 1419 Planarity : 0.005 0.046 1461 Dihedral : 5.950 28.681 1086 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.43 % Allowed : 17.17 % Favored : 78.41 % 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: -1.81 (0.24), residues: 1020 helix: 1.16 (0.22), residues: 498 sheet: -2.81 (0.40), residues: 126 loop : -3.95 (0.22), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 977 TYR 0.009 0.001 TYR A1049 PHE 0.014 0.002 PHE B1130 TRP 0.005 0.001 TRP B1084 HIS 0.003 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 8433) covalent geometry : angle 0.72308 / 0.35 (11448) SS BOND : bond 0.00389 / 0.25 ( 12) SS BOND : angle 1.15597 / 0.69 ( 24) hydrogen bonds : bond 0.04756 / 3.13 ( 471) hydrogen bonds : angle 4.82616 / 3.49 ( 1422) link_NAG-ASN : bond 0.00742 / 0.45 ( 24) link_NAG-ASN : angle 2.56737 / 1.73 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1070 TYR cc_start: 0.7171 (m-80) cc_final: 0.6827 (m-80) REVERT: B 976 ASP cc_start: 0.7857 (m-30) cc_final: 0.7178 (m-30) REVERT: C 976 ASP cc_start: 0.7562 (m-30) cc_final: 0.6908 (m-30) REVERT: C 977 ARG cc_start: 0.8541 (mtt90) cc_final: 0.8334 (mtt90) outliers start: 40 outliers final: 28 residues processed: 140 average time/residue: 0.0958 time to fit residues: 18.0805 Evaluate side-chains 118 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1112 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.070524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060587 restraints weight = 38989.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.062189 restraints weight = 24013.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.063300 restraints weight = 16816.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.064047 restraints weight = 12879.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.064640 restraints weight = 10556.962| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8469 Z= 0.175 Angle : 0.769 9.478 11544 Z= 0.369 Chirality : 0.058 0.352 1419 Planarity : 0.005 0.047 1461 Dihedral : 5.943 26.585 1086 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.21 % Allowed : 18.94 % Favored : 76.85 % 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: -1.82 (0.25), residues: 1020 helix: 1.16 (0.22), residues: 498 sheet: -2.81 (0.35), residues: 156 loop : -3.96 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 977 TYR 0.009 0.001 TYR B1120 PHE 0.016 0.002 PHE C 741 TRP 0.003 0.001 TRP B1084 HIS 0.004 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 8433) covalent geometry : angle 0.74391 / 0.36 (11448) SS BOND : bond 0.00289 / 0.18 ( 12) SS BOND : angle 1.44729 / 0.86 ( 24) hydrogen bonds : bond 0.04841 / 3.20 ( 471) hydrogen bonds : angle 4.77902 / 3.45 ( 1422) link_NAG-ASN : bond 0.00706 / 0.43 ( 24) link_NAG-ASN : angle 2.48543 / 1.68 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1065 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7548 (m-70) REVERT: B 744 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6145 (tt0) REVERT: B 1011 MET cc_start: 0.8250 (ppp) cc_final: 0.7663 (ppp) REVERT: B 1014 CYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7082 (m) REVERT: C 976 ASP cc_start: 0.7583 (m-30) cc_final: 0.7092 (m-30) REVERT: C 1011 MET cc_start: 0.8517 (ppp) cc_final: 0.8005 (ppp) outliers start: 38 outliers final: 25 residues processed: 123 average time/residue: 0.0852 time to fit residues: 14.4544 Evaluate side-chains 117 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1065 HIS Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1112 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 ASN ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.071579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061763 restraints weight = 38438.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.063322 restraints weight = 24000.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.064440 restraints weight = 16932.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.065218 restraints weight = 13084.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065742 restraints weight = 10709.013| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8469 Z= 0.145 Angle : 0.732 10.899 11544 Z= 0.349 Chirality : 0.057 0.358 1419 Planarity : 0.005 0.047 1461 Dihedral : 5.671 27.283 1086 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.99 % Allowed : 19.60 % Favored : 76.41 % 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: -1.72 (0.25), residues: 1020 helix: 1.36 (0.22), residues: 498 sheet: -2.98 (0.37), residues: 156 loop : -4.00 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 977 TYR 0.008 0.001 TYR A1049 PHE 0.013 0.001 PHE B1130 TRP 0.005 0.001 TRP A1084 HIS 0.003 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 8433) covalent geometry : angle 0.70817 / 0.34 (11448) SS BOND : bond 0.00209 / 0.11 ( 12) SS BOND : angle 1.39724 / 0.86 ( 24) hydrogen bonds : bond 0.04564 / 3.02 ( 471) hydrogen bonds : angle 4.59252 / 3.31 ( 1422) link_NAG-ASN : bond 0.00716 / 0.43 ( 24) link_NAG-ASN : angle 2.36192 / 1.58 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 982 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.7432 (mtp85) REVERT: A 1065 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7556 (m-70) REVERT: B 744 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6262 (tt0) REVERT: B 1011 MET cc_start: 0.8243 (ppp) cc_final: 0.7660 (ppp) REVERT: B 1014 CYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7094 (m) REVERT: C 976 ASP cc_start: 0.7560 (m-30) cc_final: 0.7090 (m-30) REVERT: C 1011 MET cc_start: 0.8489 (ppp) cc_final: 0.8021 (ppp) outliers start: 36 outliers final: 23 residues processed: 135 average time/residue: 0.0878 time to fit residues: 16.2612 Evaluate side-chains 122 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1065 HIS Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.071255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061428 restraints weight = 38688.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.063001 restraints weight = 24294.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.064107 restraints weight = 17247.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.064729 restraints weight = 13285.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.065391 restraints weight = 11155.032| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8469 Z= 0.167 Angle : 0.758 14.151 11544 Z= 0.364 Chirality : 0.057 0.348 1419 Planarity : 0.005 0.047 1461 Dihedral : 5.660 29.306 1086 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.43 % Allowed : 20.38 % Favored : 75.19 % 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: -1.69 (0.25), residues: 1020 helix: 1.34 (0.22), residues: 498 sheet: -2.89 (0.37), residues: 156 loop : -3.95 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 977 TYR 0.009 0.001 TYR A1049 PHE 0.016 0.002 PHE B1130 TRP 0.002 0.001 TRP B1084 HIS 0.004 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 8433) covalent geometry : angle 0.73534 / 0.36 (11448) SS BOND : bond 0.00213 / 0.11 ( 12) SS BOND : angle 1.50322 / 0.90 ( 24) hydrogen bonds : bond 0.04723 / 3.13 ( 471) hydrogen bonds : angle 4.59909 / 3.33 ( 1422) link_NAG-ASN : bond 0.00702 / 0.42 ( 24) link_NAG-ASN : angle 2.32590 / 1.55 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 744 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6578 (tt0) REVERT: A 1065 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7570 (m-70) REVERT: B 744 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6218 (tt0) REVERT: B 1011 MET cc_start: 0.8280 (ppp) cc_final: 0.7719 (ppp) REVERT: B 1014 CYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7090 (m) REVERT: C 976 ASP cc_start: 0.7472 (m-30) cc_final: 0.7143 (m-30) REVERT: C 1011 MET cc_start: 0.8499 (ppp) cc_final: 0.8078 (ppp) outliers start: 40 outliers final: 30 residues processed: 126 average time/residue: 0.1006 time to fit residues: 17.2513 Evaluate side-chains 127 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1065 HIS Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 4 optimal weight: 0.0980 chunk 86 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 ASN ** 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 = 0.3572 r_free = 0.3572 target = 0.072225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.062294 restraints weight = 38551.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.063874 restraints weight = 24296.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064986 restraints weight = 17315.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.065746 restraints weight = 13392.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.066353 restraints weight = 11036.339| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8469 Z= 0.148 Angle : 0.744 14.958 11544 Z= 0.356 Chirality : 0.057 0.346 1419 Planarity : 0.005 0.047 1461 Dihedral : 5.526 28.501 1086 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.88 % Allowed : 20.60 % Favored : 75.53 % 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: -1.53 (0.25), residues: 1020 helix: 1.47 (0.22), residues: 498 sheet: -2.77 (0.38), residues: 156 loop : -3.88 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 977 TYR 0.008 0.001 TYR A1049 PHE 0.016 0.002 PHE B1130 TRP 0.007 0.001 TRP A1084 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 8433) covalent geometry : angle 0.72329 / 0.35 (11448) SS BOND : bond 0.00190 / 0.10 ( 12) SS BOND : angle 1.28766 / 0.76 ( 24) hydrogen bonds : bond 0.04621 / 3.03 ( 471) hydrogen bonds : angle 4.50102 / 3.25 ( 1422) link_NAG-ASN : bond 0.00692 / 0.42 ( 24) link_NAG-ASN : angle 2.26550 / 1.50 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 744 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6646 (tt0) REVERT: A 976 ASP cc_start: 0.7826 (m-30) cc_final: 0.7465 (m-30) REVERT: A 982 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.7043 (mtp85) REVERT: A 1032 MET cc_start: 0.8356 (ptp) cc_final: 0.8137 (ptt) REVERT: A 1065 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7512 (m-70) REVERT: B 744 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.6130 (tt0) REVERT: B 1011 MET cc_start: 0.8267 (ppp) cc_final: 0.7683 (ppp) REVERT: B 1014 CYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7111 (m) REVERT: C 966 LEU cc_start: 0.9109 (tp) cc_final: 0.8867 (tp) REVERT: C 1011 MET cc_start: 0.8451 (ppp) cc_final: 0.8021 (ppp) outliers start: 35 outliers final: 24 residues processed: 131 average time/residue: 0.0983 time to fit residues: 17.6978 Evaluate side-chains 120 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1065 HIS Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 744 GLN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN B 942 ASN ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 ASN ** 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 = 0.3574 r_free = 0.3574 target = 0.072215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.062163 restraints weight = 38857.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063723 restraints weight = 24611.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.064828 restraints weight = 17704.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.065609 restraints weight = 13801.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.066022 restraints weight = 11403.618| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8469 Z= 0.151 Angle : 0.757 15.278 11544 Z= 0.363 Chirality : 0.057 0.341 1419 Planarity : 0.005 0.046 1461 Dihedral : 5.468 26.401 1086 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.77 % Allowed : 21.71 % Favored : 74.53 % 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: -1.34 (0.25), residues: 1020 helix: 1.45 (0.22), residues: 498 sheet: -2.36 (0.42), residues: 126 loop : -3.65 (0.23), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 977 TYR 0.009 0.001 TYR A1049 PHE 0.015 0.002 PHE A 909 TRP 0.004 0.001 TRP A1084 HIS 0.004 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 8433) covalent geometry : angle 0.73752 / 0.36 (11448) SS BOND : bond 0.00183 / 0.10 ( 12) SS BOND : angle 1.21774 / 0.72 ( 24) hydrogen bonds : bond 0.04644 / 3.05 ( 471) hydrogen bonds : angle 4.49567 / 3.23 ( 1422) link_NAG-ASN : bond 0.00688 / 0.42 ( 24) link_NAG-ASN : angle 2.21071 / 1.46 ( 72) =============================================================================== Job complete usr+sys time: 1313.21 seconds wall clock time: 23 minutes 37.97 seconds (1417.97 seconds total)