Starting phenix.real_space_refine on Sat Jul 26 01:26:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m3w_30072/07_2025/6m3w_30072.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m3w_30072/07_2025/6m3w_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6m3w_30072/07_2025/6m3w_30072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m3w_30072/07_2025/6m3w_30072.map" model { file = "/net/cci-nas-00/data/ceres_data/6m3w_30072/07_2025/6m3w_30072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m3w_30072/07_2025/6m3w_30072.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 24 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 dihedrals: 24 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.81, per 1000 atoms: 0.70 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: 2.10 Conformation dependent library (CDL) restraints added in 981.9 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: 0.78 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: 2.47 Time building geometry restraints manager: 2.50 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 - 22.13: 5035 22.13 - 44.27: 255 44.27 - 66.40: 44 66.40 - 88.54: 67 88.54 - 110.67: 44 Dihedral angle restraints: 5445 sinusoidal: 2430 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 5442 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.860 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 20.556 110.670 3447 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.006 TRP B1084 HIS 0.006 0.002 HIS B1030 PHE 0.038 0.006 PHE C 952 TYR 0.023 0.004 TYR B1029 ARG 0.011 0.002 ARG B1055 Details of bonding type rmsd link_NAG-ASN : bond 0.01558 ( 24) link_NAG-ASN : angle 5.23566 ( 72) hydrogen bonds : bond 0.13763 ( 471) hydrogen bonds : angle 7.83782 ( 1422) SS BOND : bond 0.00741 ( 12) SS BOND : angle 2.03832 ( 24) covalent geometry : bond 0.01096 ( 8433) covalent geometry : angle 1.30693 (11448) *********************** 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 : 1.994 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: 0.8308 (t80) cc_final: 0.7816 (t80) REVERT: A 1070 TYR cc_start: 0.7321 (m-80) cc_final: 0.6850 (m-80) REVERT: B 907 ASN cc_start: 0.7892 (m-40) cc_final: 0.7572 (p0) REVERT: B 989 TYR cc_start: 0.8291 (t80) cc_final: 0.7921 (t80) REVERT: C 907 ASN cc_start: 0.7800 (m-40) cc_final: 0.7354 (p0) REVERT: C 976 ASP cc_start: 0.7541 (m-30) cc_final: 0.6704 (m-30) REVERT: C 994 LEU cc_start: 0.9439 (mt) cc_final: 0.9213 (tp) REVERT: C 1130 PHE cc_start: 0.8655 (m-80) cc_final: 0.8452 (m-80) outliers start: 6 outliers final: 0 residues processed: 233 average time/residue: 0.2870 time to fit residues: 87.3280 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 : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** 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 = 0.3569 r_free = 0.3569 target = 0.071453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061993 restraints weight = 37670.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063579 restraints weight = 22676.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064700 restraints weight = 15755.837| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2982 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= 0.185 Angle : 0.905 9.177 11544 Z= 0.422 Chirality : 0.059 0.411 1419 Planarity : 0.006 0.057 1461 Dihedral : 18.135 96.729 1590 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.32 % Allowed : 11.07 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.23), residues: 1020 helix: 0.06 (0.21), residues: 492 sheet: -3.19 (0.43), residues: 117 loop : -3.67 (0.23), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP C1084 HIS 0.002 0.001 HIS C1030 PHE 0.023 0.002 PHE B1079 TYR 0.015 0.001 TYR C 989 ARG 0.006 0.001 ARG A 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00941 ( 24) link_NAG-ASN : angle 3.48654 ( 72) hydrogen bonds : bond 0.05214 ( 471) hydrogen bonds : angle 5.72391 ( 1422) SS BOND : bond 0.00435 ( 12) SS BOND : angle 1.22020 ( 24) covalent geometry : bond 0.00386 ( 8433) covalent geometry : angle 0.86429 (11448) *********************** 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 200 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.197 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: B 996 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7313 (tpt170) REVERT: B 1131 LYS cc_start: 0.8440 (mmpt) cc_final: 0.8065 (mmtm) REVERT: B 1166 ASP cc_start: 0.8144 (m-30) cc_final: 0.7716 (t0) REVERT: C 976 ASP cc_start: 0.7494 (m-30) cc_final: 0.7188 (m-30) REVERT: C 1166 ASP cc_start: 0.8132 (m-30) cc_final: 0.7816 (t0) outliers start: 39 outliers final: 18 residues processed: 187 average time/residue: 0.2324 time to fit residues: 58.2003 Evaluate side-chains 135 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1176 ASN 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 1176 ASN 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 988 THR 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 34 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 29 optimal weight: 0.0000 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 ASN ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3530 r_free = 0.3530 target = 0.069951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.060198 restraints weight = 38677.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.061743 restraints weight = 23721.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.062829 restraints weight = 16623.225| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8469 Z= 0.233 Angle : 0.895 8.869 11544 Z= 0.419 Chirality : 0.058 0.372 1419 Planarity : 0.005 0.047 1461 Dihedral : 15.178 91.689 1590 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 5.09 % Allowed : 13.40 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.24), residues: 1020 helix: 0.55 (0.21), residues: 495 sheet: -3.16 (0.41), residues: 117 loop : -3.68 (0.24), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1084 HIS 0.018 0.002 HIS B1065 PHE 0.017 0.002 PHE B1057 TYR 0.013 0.002 TYR C1029 ARG 0.006 0.001 ARG A 977 Details of bonding type rmsd link_NAG-ASN : bond 0.00878 ( 24) link_NAG-ASN : angle 3.33152 ( 72) hydrogen bonds : bond 0.05302 ( 471) hydrogen bonds : angle 5.43377 ( 1422) SS BOND : bond 0.00449 ( 12) SS BOND : angle 1.35796 ( 24) covalent geometry : bond 0.00501 ( 8433) covalent geometry : angle 0.85700 (11448) *********************** 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 163 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.964 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 936 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 1070 TYR cc_start: 0.7186 (m-80) cc_final: 0.6830 (m-80) REVERT: A 1130 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8124 (t80) REVERT: B 976 ASP cc_start: 0.7845 (m-30) cc_final: 0.7423 (m-30) REVERT: B 1130 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7927 (t80) REVERT: B 1166 ASP cc_start: 0.8168 (m-30) cc_final: 0.7880 (t0) REVERT: C 972 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: C 1130 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.7836 (t80) REVERT: C 1166 ASP cc_start: 0.8150 (m-30) cc_final: 0.7879 (t0) outliers start: 46 outliers final: 25 residues processed: 152 average time/residue: 0.2691 time to fit residues: 55.1294 Evaluate side-chains 129 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 1045 LEU Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1130 PHE 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.070311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060518 restraints weight = 38433.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.062092 restraints weight = 23656.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.063187 restraints weight = 16625.367| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8469 Z= 0.189 Angle : 0.835 8.836 11544 Z= 0.391 Chirality : 0.056 0.363 1419 Planarity : 0.005 0.061 1461 Dihedral : 13.828 87.988 1590 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.54 % Allowed : 14.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.25), residues: 1020 helix: 0.96 (0.22), residues: 492 sheet: -2.86 (0.38), residues: 135 loop : -3.64 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B1084 HIS 0.005 0.001 HIS B1065 PHE 0.014 0.002 PHE B1057 TYR 0.009 0.001 TYR A1049 ARG 0.013 0.001 ARG C 977 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 24) link_NAG-ASN : angle 3.24521 ( 72) hydrogen bonds : bond 0.05044 ( 471) hydrogen bonds : angle 5.10445 ( 1422) SS BOND : bond 0.00307 ( 12) SS BOND : angle 1.31684 ( 24) covalent geometry : bond 0.00402 ( 8433) covalent geometry : angle 0.79547 (11448) *********************** 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 157 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.884 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 936 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 1070 TYR cc_start: 0.7200 (m-80) cc_final: 0.6862 (m-80) REVERT: B 976 ASP cc_start: 0.7938 (m-30) cc_final: 0.6756 (m-30) REVERT: B 1020 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8603 (mtpp) REVERT: B 1166 ASP cc_start: 0.8099 (m-30) cc_final: 0.7859 (t0) REVERT: C 976 ASP cc_start: 0.7549 (m-30) cc_final: 0.6838 (m-30) REVERT: C 977 ARG cc_start: 0.8499 (mtt90) cc_final: 0.8132 (mtt90) REVERT: C 1130 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8209 (t80) REVERT: C 1166 ASP cc_start: 0.8158 (m-30) cc_final: 0.7950 (t0) outliers start: 41 outliers final: 28 residues processed: 140 average time/residue: 0.2908 time to fit residues: 54.0012 Evaluate side-chains 126 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 948 LEU 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 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 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 1168 LEU Chi-restraints excluded: chain B residue 1176 ASN 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 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 1092 PHE Chi-restraints excluded: chain C residue 1130 PHE Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 0 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 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 = 0.3547 r_free = 0.3547 target = 0.070973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.061289 restraints weight = 37930.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062841 restraints weight = 23293.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063924 restraints weight = 16395.064| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4601 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= 0.158 Angle : 0.774 8.753 11544 Z= 0.362 Chirality : 0.053 0.365 1419 Planarity : 0.005 0.046 1461 Dihedral : 12.772 83.776 1590 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.32 % Allowed : 15.84 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.25), residues: 1020 helix: 1.20 (0.22), residues: 495 sheet: -3.34 (0.35), residues: 156 loop : -3.91 (0.23), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1084 HIS 0.003 0.001 HIS C1046 PHE 0.012 0.002 PHE B1057 TYR 0.009 0.001 TYR C 738 ARG 0.007 0.001 ARG C 977 Details of bonding type rmsd link_NAG-ASN : bond 0.00753 ( 24) link_NAG-ASN : angle 3.08934 ( 72) hydrogen bonds : bond 0.04714 ( 471) hydrogen bonds : angle 4.82834 ( 1422) SS BOND : bond 0.00209 ( 12) SS BOND : angle 1.11119 ( 24) covalent geometry : bond 0.00334 ( 8433) covalent geometry : angle 0.73554 (11448) *********************** 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 160 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.826 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 976 ASP cc_start: 0.7696 (m-30) cc_final: 0.7372 (m-30) REVERT: B 982 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8389 (mtp85) REVERT: C 976 ASP cc_start: 0.7525 (m-30) cc_final: 0.6869 (m-30) REVERT: C 1011 MET cc_start: 0.8420 (ppp) cc_final: 0.7960 (ppp) REVERT: C 1130 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8217 (t80) outliers start: 39 outliers final: 27 residues processed: 151 average time/residue: 0.2411 time to fit residues: 47.9977 Evaluate side-chains 124 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 949 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1176 ASN 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 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 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 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 Chi-restraints excluded: chain C residue 1130 PHE 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 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.0050 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 935 ASN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.069465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059723 restraints weight = 38802.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061272 restraints weight = 23653.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.062335 restraints weight = 16559.263| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8469 Z= 0.211 Angle : 0.807 8.619 11544 Z= 0.387 Chirality : 0.053 0.335 1419 Planarity : 0.005 0.043 1461 Dihedral : 12.359 80.564 1590 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.54 % Allowed : 18.16 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.24), residues: 1020 helix: 1.07 (0.22), residues: 495 sheet: -2.66 (0.41), residues: 132 loop : -3.96 (0.22), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B1084 HIS 0.004 0.001 HIS C1030 PHE 0.015 0.002 PHE C1057 TYR 0.010 0.001 TYR B1120 ARG 0.008 0.001 ARG C1167 Details of bonding type rmsd link_NAG-ASN : bond 0.00718 ( 24) link_NAG-ASN : angle 2.98729 ( 72) hydrogen bonds : bond 0.04987 ( 471) hydrogen bonds : angle 4.87786 ( 1422) SS BOND : bond 0.00285 ( 12) SS BOND : angle 1.41188 ( 24) covalent geometry : bond 0.00450 ( 8433) covalent geometry : angle 0.77202 (11448) *********************** 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 140 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.886 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: 0.7317 (m-80) cc_final: 0.6930 (m-80) REVERT: B 977 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7542 (mmt90) REVERT: B 1011 MET cc_start: 0.8188 (ppp) cc_final: 0.7657 (ppp) REVERT: C 976 ASP cc_start: 0.7570 (m-30) cc_final: 0.6937 (m-30) REVERT: C 977 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8333 (mtt90) REVERT: C 1011 MET cc_start: 0.8454 (ppp) cc_final: 0.8003 (ppp) outliers start: 41 outliers final: 33 residues processed: 130 average time/residue: 0.2249 time to fit residues: 39.2447 Evaluate side-chains 124 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 1014 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 735 LEU 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 1084 TRP 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 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 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.070414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060880 restraints weight = 38032.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.062409 restraints weight = 23597.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.063456 restraints weight = 16664.728| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8469 Z= 0.169 Angle : 0.772 8.574 11544 Z= 0.365 Chirality : 0.052 0.325 1419 Planarity : 0.005 0.044 1461 Dihedral : 11.899 78.075 1590 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.76 % Allowed : 18.60 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.25), residues: 1020 helix: 1.17 (0.22), residues: 498 sheet: -3.15 (0.33), residues: 186 loop : -4.02 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B1084 HIS 0.004 0.001 HIS C1030 PHE 0.013 0.002 PHE C1057 TYR 0.009 0.001 TYR B1120 ARG 0.006 0.001 ARG C1073 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 24) link_NAG-ASN : angle 2.91758 ( 72) hydrogen bonds : bond 0.04764 ( 471) hydrogen bonds : angle 4.76447 ( 1422) SS BOND : bond 0.00253 ( 12) SS BOND : angle 1.23445 ( 24) covalent geometry : bond 0.00363 ( 8433) covalent geometry : angle 0.73800 (11448) *********************** 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 141 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.868 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 982 ARG cc_start: 0.8369 (ttm-80) cc_final: 0.7449 (mtp85) REVERT: A 1065 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7749 (m-70) REVERT: B 1011 MET cc_start: 0.8236 (ppp) cc_final: 0.7750 (ppp) REVERT: B 1014 CYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7160 (m) REVERT: B 1091 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8257 (p90) REVERT: C 976 ASP cc_start: 0.7552 (m-30) cc_final: 0.7039 (m-30) REVERT: C 977 ARG cc_start: 0.8574 (mtt90) cc_final: 0.8365 (mtt90) REVERT: C 1011 MET cc_start: 0.8455 (ppp) cc_final: 0.8025 (ppp) outliers start: 43 outliers final: 32 residues processed: 130 average time/residue: 0.2182 time to fit residues: 38.1089 Evaluate side-chains 125 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 925 THR 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 1014 CYS Chi-restraints excluded: chain A residue 1045 LEU 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 735 LEU 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 1045 LEU Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1091 PHE Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1126 GLU 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 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 Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** 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 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** 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 = 0.3540 r_free = 0.3540 target = 0.070063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.060384 restraints weight = 38658.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.061946 restraints weight = 23882.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.063042 restraints weight = 16797.954| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8469 Z= 0.187 Angle : 0.773 10.779 11544 Z= 0.370 Chirality : 0.052 0.309 1419 Planarity : 0.005 0.044 1461 Dihedral : 11.493 74.866 1590 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.98 % Allowed : 19.27 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.25), residues: 1020 helix: 1.18 (0.22), residues: 498 sheet: -2.72 (0.36), residues: 156 loop : -3.88 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C1084 HIS 0.004 0.001 HIS C1030 PHE 0.013 0.002 PHE C1057 TYR 0.009 0.001 TYR B1120 ARG 0.007 0.001 ARG A 977 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 24) link_NAG-ASN : angle 2.86180 ( 72) hydrogen bonds : bond 0.04824 ( 471) hydrogen bonds : angle 4.73957 ( 1422) SS BOND : bond 0.00262 ( 12) SS BOND : angle 1.58567 ( 24) covalent geometry : bond 0.00401 ( 8433) covalent geometry : angle 0.73836 (11448) *********************** 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 139 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 0.851 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: 0.8409 (ttm-80) cc_final: 0.7473 (mtp85) REVERT: A 1070 TYR cc_start: 0.7216 (m-80) cc_final: 0.6864 (m-80) REVERT: B 744 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6304 (tt0) REVERT: B 1011 MET cc_start: 0.8295 (ppp) cc_final: 0.7801 (ppp) REVERT: B 1014 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7198 (m) REVERT: C 976 ASP cc_start: 0.7589 (m-30) cc_final: 0.7169 (m-30) REVERT: C 977 ARG cc_start: 0.8593 (mtt90) cc_final: 0.8382 (mtt90) REVERT: C 1011 MET cc_start: 0.8473 (ppp) cc_final: 0.8057 (ppp) outliers start: 45 outliers final: 31 residues processed: 128 average time/residue: 0.2028 time to fit residues: 35.6379 Evaluate side-chains 118 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 1045 LEU Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 735 LEU 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 990 VAL Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1045 LEU 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 1076 VAL Chi-restraints excluded: chain C residue 1087 THR Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1112 ILE 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 79 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** 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 935 ASN ** 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 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** 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 = 0.3564 r_free = 0.3564 target = 0.071124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.061506 restraints weight = 38410.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.063073 restraints weight = 23654.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.064184 restraints weight = 16601.553| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8469 Z= 0.152 Angle : 0.755 12.934 11544 Z= 0.358 Chirality : 0.052 0.307 1419 Planarity : 0.005 0.044 1461 Dihedral : 10.961 72.225 1590 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.99 % Allowed : 20.71 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.25), residues: 1020 helix: 1.33 (0.22), residues: 498 sheet: -2.87 (0.34), residues: 186 loop : -3.99 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1084 HIS 0.003 0.001 HIS B1030 PHE 0.013 0.002 PHE C 741 TYR 0.009 0.001 TYR A 989 ARG 0.007 0.001 ARG A 977 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 24) link_NAG-ASN : angle 2.81723 ( 72) hydrogen bonds : bond 0.04596 ( 471) hydrogen bonds : angle 4.55841 ( 1422) SS BOND : bond 0.00223 ( 12) SS BOND : angle 1.25017 ( 24) covalent geometry : bond 0.00325 ( 8433) covalent geometry : angle 0.72267 (11448) *********************** 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 136 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.953 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: 0.6064 (tt0) REVERT: A 982 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.7179 (mtp85) REVERT: B 744 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.6244 (tt0) REVERT: B 1011 MET cc_start: 0.8259 (ppp) cc_final: 0.7760 (ppp) REVERT: B 1014 CYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7194 (m) REVERT: C 918 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8029 (pp20) REVERT: C 976 ASP cc_start: 0.7564 (m-30) cc_final: 0.7209 (m-30) REVERT: C 1011 MET cc_start: 0.8506 (ppp) cc_final: 0.8113 (ppp) outliers start: 36 outliers final: 26 residues processed: 126 average time/residue: 0.2190 time to fit residues: 37.3308 Evaluate side-chains 123 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 744 GLN 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 1014 CYS Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 735 LEU 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 B residue 1112 ILE Chi-restraints excluded: chain B residue 1126 GLU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 918 GLU 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 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** 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 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** 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 = 0.3557 r_free = 0.3557 target = 0.070828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.061230 restraints weight = 38182.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062783 restraints weight = 23913.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.063879 restraints weight = 16860.492| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8469 Z= 0.165 Angle : 0.770 15.072 11544 Z= 0.367 Chirality : 0.052 0.297 1419 Planarity : 0.005 0.045 1461 Dihedral : 10.668 69.098 1590 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.54 % Allowed : 21.48 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.25), residues: 1020 helix: 1.34 (0.22), residues: 498 sheet: -2.84 (0.34), residues: 186 loop : -3.98 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B1084 HIS 0.005 0.001 HIS C1030 PHE 0.015 0.002 PHE B 909 TYR 0.032 0.001 TYR B 738 ARG 0.011 0.001 ARG C 977 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 24) link_NAG-ASN : angle 2.77650 ( 72) hydrogen bonds : bond 0.04588 ( 471) hydrogen bonds : angle 4.59150 ( 1422) SS BOND : bond 0.00211 ( 12) SS BOND : angle 1.46092 ( 24) covalent geometry : bond 0.00357 ( 8433) covalent geometry : angle 0.73773 (11448) ********************** 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 127 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.952 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 744 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: A 1070 TYR cc_start: 0.7268 (m-80) cc_final: 0.6940 (m-80) REVERT: B 744 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6267 (tt0) REVERT: B 1011 MET cc_start: 0.8292 (ppp) cc_final: 0.7805 (ppp) REVERT: B 1014 CYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7212 (m) REVERT: C 918 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8055 (pp20) REVERT: C 976 ASP cc_start: 0.7602 (m-30) cc_final: 0.7371 (m-30) REVERT: C 1011 MET cc_start: 0.8531 (ppp) cc_final: 0.8155 (ppp) outliers start: 32 outliers final: 25 residues processed: 117 average time/residue: 0.2101 time to fit residues: 33.7920 Evaluate side-chains 116 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 744 GLN 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 1014 CYS Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 735 LEU 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 B residue 1112 ILE Chi-restraints excluded: chain C residue 918 GLU 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 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 ASN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 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 = 0.3514 r_free = 0.3514 target = 0.069016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.059313 restraints weight = 38893.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060869 restraints weight = 24148.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.061959 restraints weight = 17105.714| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8469 Z= 0.238 Angle : 0.822 13.967 11544 Z= 0.398 Chirality : 0.052 0.269 1419 Planarity : 0.005 0.043 1461 Dihedral : 10.653 65.938 1590 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.99 % Allowed : 21.71 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.25), residues: 1020 helix: 1.12 (0.21), residues: 498 sheet: -2.69 (0.35), residues: 156 loop : -3.85 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B1084 HIS 0.006 0.001 HIS C1030 PHE 0.016 0.002 PHE C1057 TYR 0.016 0.002 TYR B 738 ARG 0.015 0.001 ARG C 977 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 24) link_NAG-ASN : angle 2.77892 ( 72) hydrogen bonds : bond 0.05052 ( 471) hydrogen bonds : angle 4.84030 ( 1422) SS BOND : bond 0.00299 ( 12) SS BOND : angle 1.58187 ( 24) covalent geometry : bond 0.00510 ( 8433) covalent geometry : angle 0.79233 (11448) =============================================================================== Job complete usr+sys time: 2757.83 seconds wall clock time: 50 minutes 17.23 seconds (3017.23 seconds total)