Starting phenix.real_space_refine on Wed Feb 12 18:55:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m3w_30072/02_2025/6m3w_30072.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m3w_30072/02_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_30072/02_2025/6m3w_30072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m3w_30072/02_2025/6m3w_30072.map" model { file = "/net/cci-nas-00/data/ceres_data/6m3w_30072/02_2025/6m3w_30072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m3w_30072/02_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-5592/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: 5.55, per 1000 atoms: 0.67 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: 2.12 Conformation dependent library (CDL) restraints added in 925.2 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: 0.69 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: 2.28 Time building geometry restraints manager: 2.44 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: 0.06 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.610 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.600 ------------------------------------------------------------------------------- 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 8433 Z= 0.726 Angle : 1.307 10.499 11448 Z= 0.688 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 227 time to evaluate : 0.937 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: 0.2467 time to fit residues: 75.1974 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 : 1.146 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061990 restraints weight = 37670.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063580 restraints weight = 22709.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064693 restraints weight = 15803.477| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 8433 Z= 0.254 Angle : 0.864 9.015 11448 Z= 0.413 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 *********************** 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 : 0.899 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: 0.7516 (ttm-80) cc_final: 0.7316 (tpt170) REVERT: B 1131 LYS cc_start: 0.8440 (mmpt) cc_final: 0.8066 (mmtm) REVERT: B 1166 ASP cc_start: 0.8150 (m-30) cc_final: 0.7721 (t0) REVERT: C 976 ASP cc_start: 0.7492 (m-30) cc_final: 0.7186 (m-30) REVERT: C 1166 ASP cc_start: 0.8135 (m-30) cc_final: 0.7820 (t0) outliers start: 39 outliers final: 18 residues processed: 187 average time/residue: 0.2155 time to fit residues: 53.8891 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 : 0.975 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 0.9990 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: 4.9990 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 = 0.069952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060189 restraints weight = 38681.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.061756 restraints weight = 23783.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062809 restraints weight = 16614.126| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8433 Z= 0.325 Angle : 0.857 8.944 11448 Z= 0.410 Chirality : 0.058 0.372 1419 Planarity : 0.005 0.047 1461 Dihedral : 15.184 91.704 1590 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.98 % Allowed : 13.40 % Favored : 81.62 % 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 0.018 0.002 PHE B1057 TYR 0.013 0.002 TYR C1029 ARG 0.006 0.001 ARG A 977 *********************** 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 162 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 117 time to evaluate : 0.900 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: A 936 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 1070 TYR cc_start: 0.7198 (m-80) cc_final: 0.6825 (m-80) REVERT: A 1130 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8139 (t80) REVERT: B 976 ASP cc_start: 0.7856 (m-30) cc_final: 0.7439 (m-30) REVERT: B 1130 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7937 (t80) REVERT: B 1166 ASP cc_start: 0.8170 (m-30) cc_final: 0.7881 (t0) REVERT: C 972 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: C 1130 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.7852 (t80) REVERT: C 1166 ASP cc_start: 0.8154 (m-30) cc_final: 0.7882 (t0) outliers start: 45 outliers final: 24 residues processed: 151 average time/residue: 0.2184 time to fit residues: 44.5328 Evaluate side-chains 127 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 ILE 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: 2.9990 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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** A1090 ASN ** 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** B1169 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.069428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.059585 restraints weight = 38631.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.061123 restraints weight = 23842.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.062206 restraints weight = 16785.331| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8433 Z= 0.319 Angle : 0.827 8.827 11448 Z= 0.400 Chirality : 0.056 0.364 1419 Planarity : 0.005 0.049 1461 Dihedral : 13.908 87.515 1590 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 5.20 % Allowed : 14.40 % Favored : 80.40 % 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: -2.03 (0.25), residues: 1020 helix: 0.82 (0.22), residues: 492 sheet: -2.92 (0.40), residues: 123 loop : -3.73 (0.24), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C1084 HIS 0.004 0.001 HIS B1065 PHE 0.017 0.002 PHE B1057 TYR 0.010 0.001 TYR B1120 ARG 0.011 0.001 ARG C 977 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1070 TYR cc_start: 0.7317 (m-80) cc_final: 0.6935 (m-80) REVERT: B 976 ASP cc_start: 0.7972 (m-30) cc_final: 0.6824 (m-30) REVERT: B 1020 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.7910 (mtpp) REVERT: B 1074 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6393 (tm-30) REVERT: B 1130 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8124 (t80) REVERT: B 1166 ASP cc_start: 0.8156 (m-30) cc_final: 0.7878 (t0) REVERT: C 976 ASP cc_start: 0.7587 (m-30) cc_final: 0.6958 (m-30) REVERT: C 977 ARG cc_start: 0.8624 (mtt90) cc_final: 0.8255 (mtt90) REVERT: C 1130 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8195 (t80) REVERT: C 1166 ASP cc_start: 0.8163 (m-30) cc_final: 0.7892 (t0) outliers start: 47 outliers final: 33 residues processed: 137 average time/residue: 0.2228 time to fit residues: 41.4433 Evaluate side-chains 128 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 1168 LEU Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1084 TRP Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1130 PHE Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain 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 949 SER Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1130 PHE Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 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 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3539 r_free = 0.3539 target = 0.070560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.060906 restraints weight = 37998.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.062457 restraints weight = 23283.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.063545 restraints weight = 16364.427| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8433 Z= 0.233 Angle : 0.750 8.762 11448 Z= 0.361 Chirality : 0.054 0.361 1419 Planarity : 0.005 0.047 1461 Dihedral : 12.865 83.716 1590 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.32 % Allowed : 16.17 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % 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: -1.96 (0.25), residues: 1020 helix: 1.13 (0.22), residues: 495 sheet: -3.19 (0.35), residues: 162 loop : -3.97 (0.23), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1084 HIS 0.003 0.001 HIS C1030 PHE 0.012 0.002 PHE C1057 TYR 0.008 0.001 TYR C 738 ARG 0.009 0.001 ARG C 977 *********************** 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 157 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1070 TYR cc_start: 0.7211 (m-80) cc_final: 0.6864 (m-80) REVERT: B 977 ARG cc_start: 0.8196 (mmt90) cc_final: 0.7669 (mmt90) REVERT: C 976 ASP cc_start: 0.7588 (m-30) cc_final: 0.7234 (m-30) outliers start: 39 outliers final: 27 residues processed: 147 average time/residue: 0.2426 time to fit residues: 47.0591 Evaluate side-chains 119 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 A residue 1176 ASN 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 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE 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 994 LEU Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1074 GLU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE 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: 0.7980 chunk 68 optimal weight: 0.0370 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- 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 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.070439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060587 restraints weight = 38610.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.062146 restraints weight = 23776.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.063244 restraints weight = 16737.818| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8433 Z= 0.250 Angle : 0.760 8.659 11448 Z= 0.371 Chirality : 0.053 0.342 1419 Planarity : 0.005 0.045 1461 Dihedral : 12.391 81.056 1590 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.21 % Allowed : 17.50 % Favored : 78.29 % 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: -1.86 (0.24), residues: 1020 helix: 1.09 (0.22), residues: 495 sheet: -2.84 (0.39), residues: 126 loop : -3.86 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B1084 HIS 0.004 0.001 HIS C1030 PHE 0.016 0.002 PHE C 741 TYR 0.009 0.001 TYR A 989 ARG 0.011 0.001 ARG A 977 *********************** 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 137 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.932 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: A 1070 TYR cc_start: 0.7273 (m-80) cc_final: 0.6903 (m-80) REVERT: B 1011 MET cc_start: 0.8150 (ppp) cc_final: 0.7577 (ppp) REVERT: C 977 ARG cc_start: 0.8580 (mtt90) cc_final: 0.8303 (mtt90) REVERT: C 1011 MET cc_start: 0.8504 (ppp) cc_final: 0.7993 (ppp) REVERT: C 1167 ARG cc_start: 0.7621 (ptp90) cc_final: 0.7383 (ttp80) outliers start: 38 outliers final: 30 residues processed: 127 average time/residue: 0.2304 time to fit residues: 39.0336 Evaluate side-chains 120 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 1076 VAL Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 0.0040 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8794 ------------------------------------------------------------------------------- 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 746 ASN ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.070603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060948 restraints weight = 38286.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.062433 restraints weight = 23832.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063513 restraints weight = 16947.846| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8433 Z= 0.232 Angle : 0.731 8.995 11448 Z= 0.354 Chirality : 0.052 0.328 1419 Planarity : 0.005 0.044 1461 Dihedral : 11.848 77.732 1590 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.98 % Allowed : 17.17 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.69 (0.25), residues: 1020 helix: 1.28 (0.22), residues: 495 sheet: -2.76 (0.36), residues: 156 loop : -3.88 (0.24), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B1084 HIS 0.003 0.001 HIS C1030 PHE 0.013 0.002 PHE B1130 TYR 0.009 0.001 TYR A 989 ARG 0.009 0.001 ARG A1073 *********************** 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 147 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.966 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: 0.8178 (tm-30) cc_final: 0.7907 (tm-30) REVERT: A 976 ASP cc_start: 0.7504 (m-30) cc_final: 0.7025 (m-30) REVERT: A 1065 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7705 (m-70) REVERT: B 744 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.5841 (tt0) REVERT: B 1011 MET cc_start: 0.8213 (ppp) cc_final: 0.7698 (ppp) REVERT: B 1014 CYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7119 (m) REVERT: B 1091 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8340 (p90) REVERT: B 1127 LEU cc_start: 0.8253 (mt) cc_final: 0.8035 (tp) REVERT: C 976 ASP cc_start: 0.7594 (m-30) cc_final: 0.7320 (m-30) REVERT: C 977 ARG cc_start: 0.8548 (mtt90) cc_final: 0.8328 (mtt90) REVERT: C 1011 MET cc_start: 0.8444 (ppp) cc_final: 0.8008 (ppp) outliers start: 45 outliers final: 31 residues processed: 134 average time/residue: 0.2226 time to fit residues: 40.1202 Evaluate side-chains 126 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 1065 HIS Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 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 1091 PHE 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 1045 LEU Chi-restraints excluded: chain C residue 1071 PHE 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 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: 0.0980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 GLN ** 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 = 0.3574 r_free = 0.3574 target = 0.071714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.062057 restraints weight = 38469.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063594 restraints weight = 24067.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064650 restraints weight = 17079.789| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8433 Z= 0.207 Angle : 0.719 11.142 11448 Z= 0.349 Chirality : 0.052 0.320 1419 Planarity : 0.005 0.051 1461 Dihedral : 11.325 74.971 1590 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.54 % Allowed : 19.49 % Favored : 75.97 % 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: -1.62 (0.25), residues: 1020 helix: 1.41 (0.22), residues: 498 sheet: -2.96 (0.37), residues: 156 loop : -3.88 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1084 HIS 0.004 0.001 HIS C1030 PHE 0.012 0.001 PHE B1130 TYR 0.009 0.001 TYR A 989 ARG 0.007 0.001 ARG C1167 *********************** 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 146 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.986 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: A 936 GLN cc_start: 0.8226 (tm-30) cc_final: 0.8020 (tm-30) REVERT: A 976 ASP cc_start: 0.7609 (m-30) cc_final: 0.7304 (m-30) REVERT: A 982 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.7283 (mtp85) REVERT: A 1065 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7742 (m-70) REVERT: B 744 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.6193 (tt0) REVERT: B 1011 MET cc_start: 0.8184 (ppp) cc_final: 0.7690 (ppp) REVERT: B 1014 CYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7155 (m) REVERT: C 977 ARG cc_start: 0.8507 (mtt90) cc_final: 0.8305 (mtt90) REVERT: C 1011 MET cc_start: 0.8439 (ppp) cc_final: 0.8014 (ppp) REVERT: C 1126 GLU cc_start: 0.5183 (OUTLIER) cc_final: 0.4970 (pp20) outliers start: 41 outliers final: 26 residues processed: 138 average time/residue: 0.2203 time to fit residues: 41.3254 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 : 0.920 ------------------------------------------------------------------------------- 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 1065 HIS Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 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 C residue 725 CYS Chi-restraints excluded: chain C residue 936 GLN 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 1045 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1126 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 0.0770 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3559 r_free = 0.3559 target = 0.070997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061318 restraints weight = 38601.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062888 restraints weight = 23906.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063980 restraints weight = 16820.177| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8433 Z= 0.243 Angle : 0.732 13.818 11448 Z= 0.358 Chirality : 0.051 0.303 1419 Planarity : 0.005 0.044 1461 Dihedral : 11.051 72.478 1590 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.65 % Allowed : 19.71 % Favored : 75.64 % 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: -1.61 (0.25), residues: 1020 helix: 1.41 (0.22), residues: 498 sheet: -2.97 (0.37), residues: 156 loop : -3.86 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B1084 HIS 0.005 0.001 HIS A1030 PHE 0.020 0.002 PHE A 909 TYR 0.011 0.001 TYR B 989 ARG 0.008 0.001 ARG B 977 *********************** 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 133 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 0.915 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: A 1065 HIS cc_start: 0.8038 (OUTLIER) cc_final: 0.7744 (m-70) REVERT: B 744 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.6256 (tt0) REVERT: B 1011 MET cc_start: 0.8248 (ppp) cc_final: 0.7801 (ppp) REVERT: B 1014 CYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7170 (m) REVERT: C 1011 MET cc_start: 0.8472 (ppp) cc_final: 0.8057 (ppp) outliers start: 42 outliers final: 26 residues processed: 125 average time/residue: 0.1880 time to fit residues: 33.4863 Evaluate side-chains 112 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 744 GLN Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1045 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 0.0970 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** 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 935 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 = 0.3571 r_free = 0.3571 target = 0.071367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.061642 restraints weight = 38049.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.063231 restraints weight = 23489.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.064319 restraints weight = 16545.954| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8433 Z= 0.227 Angle : 0.742 14.732 11448 Z= 0.363 Chirality : 0.051 0.301 1419 Planarity : 0.005 0.055 1461 Dihedral : 10.788 70.645 1590 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.99 % Allowed : 21.04 % 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: -1.52 (0.25), residues: 1020 helix: 1.47 (0.22), residues: 498 sheet: -2.89 (0.37), residues: 156 loop : -3.82 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1084 HIS 0.004 0.001 HIS A1030 PHE 0.019 0.002 PHE A 909 TYR 0.011 0.001 TYR B 989 ARG 0.016 0.001 ARG C 977 ********************** 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 131 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.867 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: A 972 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: A 982 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.8025 (mtp85) REVERT: A 1070 TYR cc_start: 0.7264 (m-80) cc_final: 0.6965 (m-80) REVERT: B 702 ILE cc_start: 0.9264 (mm) cc_final: 0.9060 (tt) REVERT: B 744 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6274 (tt0) REVERT: B 1011 MET cc_start: 0.8304 (ppp) cc_final: 0.7811 (ppp) REVERT: B 1014 CYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7238 (m) REVERT: C 1011 MET cc_start: 0.8489 (ppp) cc_final: 0.8084 (ppp) outliers start: 36 outliers final: 26 residues processed: 121 average time/residue: 0.1965 time to fit residues: 33.2254 Evaluate side-chains 113 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 936 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 972 GLU 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 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 744 GLN Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1045 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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** ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.068673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.058935 restraints weight = 38966.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.060456 restraints weight = 24238.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.061523 restraints weight = 17211.020| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8433 Z= 0.398 Angle : 0.842 13.393 11448 Z= 0.423 Chirality : 0.054 0.275 1419 Planarity : 0.006 0.062 1461 Dihedral : 10.891 67.488 1590 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 4.10 % Allowed : 21.82 % Favored : 74.09 % 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: -1.84 (0.24), residues: 1020 helix: 1.02 (0.21), residues: 498 sheet: -2.68 (0.35), residues: 156 loop : -3.83 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C1084 HIS 0.006 0.002 HIS C1030 PHE 0.019 0.002 PHE A 909 TYR 0.010 0.002 TYR B1120 ARG 0.011 0.001 ARG C 977 =============================================================================== Job complete usr+sys time: 2406.89 seconds wall clock time: 44 minutes 24.02 seconds (2664.02 seconds total)