Starting phenix.real_space_refine on Wed Mar 12 19:39:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m3w_30072/03_2025/6m3w_30072.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m3w_30072/03_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_30072/03_2025/6m3w_30072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m3w_30072/03_2025/6m3w_30072.map" model { file = "/net/cci-nas-00/data/ceres_data/6m3w_30072/03_2025/6m3w_30072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m3w_30072/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.25, per 1000 atoms: 0.75 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.76 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: 2.61 Time building geometry restraints manager: 2.62 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: 30.720 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.150 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.820 ------------------------------------------------------------------------------- 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 : 1.015 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: 0.2783 time to fit residues: 84.6102 Evaluate side-chains 126 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN A1090 ASN A1141 HIS ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN B1065 HIS ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 ASN C 993 GLN C1090 ASN C1141 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.071453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061993 restraints weight = 37670.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063579 restraints weight = 22676.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064700 restraints weight = 15755.837| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 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 : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 996 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7313 (tpt170) REVERT: B 1131 LYS cc_start: 0.8440 (mmpt) cc_final: 0.8065 (mmtm) REVERT: B 1166 ASP cc_start: 0.8144 (m-30) cc_final: 0.7716 (t0) REVERT: C 976 ASP cc_start: 0.7494 (m-30) cc_final: 0.7188 (m-30) REVERT: C 1166 ASP cc_start: 0.8132 (m-30) cc_final: 0.7816 (t0) outliers start: 39 outliers final: 18 residues processed: 187 average time/residue: 0.2211 time to fit residues: 55.5465 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 : 0.906 ------------------------------------------------------------------------------- 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 = 0.069951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.060198 restraints weight = 38677.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.061743 restraints weight = 23721.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.062829 restraints weight = 16623.225| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8433 Z= 0.325 Angle : 0.857 8.869 11448 Z= 0.411 Chirality : 0.058 0.372 1419 Planarity : 0.005 0.047 1461 Dihedral : 15.178 91.689 1590 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 5.09 % Allowed : 13.40 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.24), residues: 1020 helix: 0.55 (0.21), residues: 495 sheet: -3.16 (0.41), residues: 117 loop : -3.68 (0.24), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1084 HIS 0.018 0.002 HIS B1065 PHE 0.017 0.002 PHE B1057 TYR 0.013 0.002 TYR C1029 ARG 0.006 0.001 ARG A 977 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 936 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 1070 TYR cc_start: 0.7186 (m-80) cc_final: 0.6830 (m-80) REVERT: A 1130 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8124 (t80) REVERT: B 976 ASP cc_start: 0.7845 (m-30) cc_final: 0.7423 (m-30) REVERT: B 1130 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7927 (t80) REVERT: B 1166 ASP cc_start: 0.8168 (m-30) cc_final: 0.7880 (t0) REVERT: C 972 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: C 1130 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.7836 (t80) REVERT: C 1166 ASP cc_start: 0.8150 (m-30) cc_final: 0.7879 (t0) outliers start: 46 outliers final: 25 residues processed: 152 average time/residue: 0.2097 time to fit residues: 43.1126 Evaluate side-chains 129 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1130 PHE Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1084 TRP Chi-restraints excluded: chain B residue 1130 PHE Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1130 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 0.0970 chunk 80 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 ASN ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.070734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.060965 restraints weight = 38411.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062537 restraints weight = 23594.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.063645 restraints weight = 16590.392| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8433 Z= 0.244 Angle : 0.784 8.886 11448 Z= 0.376 Chirality : 0.055 0.365 1419 Planarity : 0.005 0.059 1461 Dihedral : 13.731 87.916 1590 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.99 % Allowed : 15.17 % Favored : 80.84 % 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: -1.80 (0.25), residues: 1020 helix: 1.03 (0.22), residues: 492 sheet: -2.83 (0.39), residues: 135 loop : -3.63 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B1084 HIS 0.005 0.001 HIS B1065 PHE 0.013 0.002 PHE B1057 TYR 0.010 0.001 TYR C 738 ARG 0.012 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 159 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.928 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 936 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7704 (tm-30) REVERT: A 976 ASP cc_start: 0.7701 (m-30) cc_final: 0.7299 (m-30) REVERT: B 976 ASP cc_start: 0.7932 (m-30) cc_final: 0.6834 (m-30) REVERT: B 982 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8366 (mtp85) REVERT: B 1020 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8612 (mtpp) REVERT: B 1166 ASP cc_start: 0.8111 (m-30) cc_final: 0.7886 (t0) REVERT: C 976 ASP cc_start: 0.7534 (m-30) cc_final: 0.6796 (m-30) REVERT: C 977 ARG cc_start: 0.8527 (mtt90) cc_final: 0.8162 (mtt90) REVERT: C 1130 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8127 (t80) outliers start: 36 outliers final: 22 residues processed: 145 average time/residue: 0.2566 time to fit residues: 48.2852 Evaluate side-chains 121 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1084 TRP Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1130 PHE 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: 1.9990 chunk 22 optimal weight: 0.0010 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 0 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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** A1090 ASN ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.069916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.060201 restraints weight = 38336.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.061734 restraints weight = 23412.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.062812 restraints weight = 16482.610| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8433 Z= 0.265 Angle : 0.764 8.744 11448 Z= 0.371 Chirality : 0.054 0.359 1419 Planarity : 0.005 0.046 1461 Dihedral : 12.962 84.125 1590 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.54 % Allowed : 16.39 % Favored : 79.07 % 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: -1.80 (0.25), residues: 1020 helix: 1.12 (0.22), residues: 492 sheet: -2.78 (0.39), residues: 132 loop : -3.78 (0.23), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B1084 HIS 0.003 0.001 HIS A1030 PHE 0.014 0.002 PHE B1057 TYR 0.010 0.001 TYR B1120 ARG 0.008 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 147 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.882 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 976 ASP cc_start: 0.7566 (m-30) cc_final: 0.4896 (m-30) REVERT: A 1070 TYR cc_start: 0.7215 (m-80) cc_final: 0.6881 (m-80) REVERT: B 977 ARG cc_start: 0.8138 (mmt90) cc_final: 0.7486 (mmt90) REVERT: B 1020 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8643 (mttm) REVERT: C 976 ASP cc_start: 0.7497 (m-30) cc_final: 0.6860 (m-30) REVERT: C 1011 MET cc_start: 0.8470 (ppp) cc_final: 0.7966 (ppp) REVERT: C 1130 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8268 (t80) REVERT: C 1167 ARG cc_start: 0.7684 (ptp90) cc_final: 0.7431 (ttp80) outliers start: 41 outliers final: 30 residues processed: 137 average time/residue: 0.2400 time to fit residues: 43.6767 Evaluate side-chains 124 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 1020 LYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1020 LYS 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 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 1112 ILE Chi-restraints excluded: chain C residue 1130 PHE Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 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 = 0.3535 r_free = 0.3535 target = 0.070371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060571 restraints weight = 38613.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.062141 restraints weight = 23639.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.063249 restraints weight = 16597.913| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4889 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 : 0.734 8.659 11448 Z= 0.359 Chirality : 0.053 0.342 1419 Planarity : 0.005 0.043 1461 Dihedral : 12.295 80.971 1590 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.54 % Allowed : 17.72 % Favored : 77.74 % 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: -1.76 (0.24), residues: 1020 helix: 1.18 (0.22), residues: 495 sheet: -2.81 (0.40), residues: 126 loop : -3.83 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B1084 HIS 0.003 0.001 HIS C1030 PHE 0.013 0.002 PHE C1057 TYR 0.010 0.001 TYR A 989 ARG 0.006 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 144 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 0.882 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: 0.7263 (m-80) cc_final: 0.6885 (m-80) REVERT: B 1011 MET cc_start: 0.8147 (ppp) cc_final: 0.7626 (ppp) REVERT: B 1166 ASP cc_start: 0.8144 (m-30) cc_final: 0.7795 (t0) REVERT: C 976 ASP cc_start: 0.7542 (m-30) cc_final: 0.6973 (m-30) REVERT: C 977 ARG cc_start: 0.8588 (mtt90) cc_final: 0.8290 (mtt90) REVERT: C 1011 MET cc_start: 0.8421 (ppp) cc_final: 0.8001 (ppp) REVERT: C 1167 ARG cc_start: 0.7733 (ptp90) cc_final: 0.7506 (ttp80) outliers start: 41 outliers final: 30 residues processed: 133 average time/residue: 0.2306 time to fit residues: 40.8905 Evaluate side-chains 123 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 1020 LYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1084 TRP Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain 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 1020 LYS Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN ** 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 = 0.3543 r_free = 0.3543 target = 0.070175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.060588 restraints weight = 38003.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.062125 restraints weight = 23653.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.063189 restraints weight = 16748.248| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8433 Z= 0.263 Angle : 0.744 9.701 11448 Z= 0.364 Chirality : 0.052 0.324 1419 Planarity : 0.005 0.044 1461 Dihedral : 11.888 77.799 1590 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 5.20 % Allowed : 17.39 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.25), residues: 1020 helix: 1.22 (0.22), residues: 495 sheet: -2.82 (0.35), residues: 156 loop : -3.84 (0.24), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B1084 HIS 0.004 0.001 HIS C1030 PHE 0.013 0.002 PHE C1057 TYR 0.009 0.001 TYR B1120 ARG 0.006 0.001 ARG A 977 *********************** 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 146 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 99 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1070 TYR cc_start: 0.7121 (m-80) cc_final: 0.6813 (m-80) REVERT: B 744 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6291 (tt0) REVERT: B 1011 MET cc_start: 0.8218 (ppp) cc_final: 0.7729 (ppp) REVERT: B 1014 CYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7188 (m) REVERT: C 976 ASP cc_start: 0.7550 (m-30) cc_final: 0.6850 (m-30) REVERT: C 977 ARG cc_start: 0.8570 (mtt90) cc_final: 0.8249 (mtt90) REVERT: C 1011 MET cc_start: 0.8458 (ppp) cc_final: 0.8023 (ppp) REVERT: C 1167 ARG cc_start: 0.7736 (ptp90) cc_final: 0.7519 (ttp80) outliers start: 47 outliers final: 33 residues processed: 134 average time/residue: 0.2319 time to fit residues: 41.5969 Evaluate side-chains 131 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 1020 LYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain 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 1045 LEU Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1084 TRP Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 2 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN ** B 744 GLN ** 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 942 ASN ** 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 = 0.3572 r_free = 0.3572 target = 0.071497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.061852 restraints weight = 38179.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063433 restraints weight = 23667.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064535 restraints weight = 16691.611| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8433 Z= 0.210 Angle : 0.707 10.986 11448 Z= 0.345 Chirality : 0.052 0.321 1419 Planarity : 0.005 0.043 1461 Dihedral : 11.366 75.389 1590 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.10 % Allowed : 20.04 % Favored : 75.86 % 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: -1.66 (0.25), residues: 1020 helix: 1.41 (0.22), residues: 498 sheet: -2.94 (0.34), residues: 186 loop : -3.98 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1084 HIS 0.003 0.001 HIS A1046 PHE 0.012 0.002 PHE B 741 TYR 0.009 0.001 TYR A 989 ARG 0.006 0.001 ARG A 977 *********************** 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 147 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 909 PHE cc_start: 0.7615 (m-80) cc_final: 0.7341 (m-80) REVERT: A 982 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.7345 (mtp85) REVERT: B 744 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.6270 (tt0) REVERT: B 1011 MET cc_start: 0.8222 (ppp) cc_final: 0.7749 (ppp) REVERT: B 1014 CYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7195 (m) REVERT: C 918 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7934 (pp20) REVERT: C 976 ASP cc_start: 0.7383 (m-30) cc_final: 0.7014 (m-30) REVERT: C 977 ARG cc_start: 0.8507 (mtt90) cc_final: 0.8278 (mtt90) REVERT: C 1011 MET cc_start: 0.8470 (ppp) cc_final: 0.8054 (ppp) outliers start: 37 outliers final: 20 residues processed: 139 average time/residue: 0.2262 time to fit residues: 42.0670 Evaluate side-chains 121 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 986 LEU Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** 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 942 ASN ** 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 = 0.3565 r_free = 0.3565 target = 0.071296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.061668 restraints weight = 38396.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.063245 restraints weight = 23796.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.064350 restraints weight = 16784.738| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8433 Z= 0.224 Angle : 0.725 14.093 11448 Z= 0.355 Chirality : 0.052 0.305 1419 Planarity : 0.005 0.044 1461 Dihedral : 10.991 73.035 1590 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.32 % Allowed : 20.04 % 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: -1.63 (0.25), residues: 1020 helix: 1.40 (0.22), residues: 498 sheet: -2.86 (0.34), residues: 186 loop : -3.96 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B1084 HIS 0.003 0.001 HIS C1030 PHE 0.018 0.002 PHE B 909 TYR 0.016 0.001 TYR B 738 ARG 0.007 0.001 ARG A 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 136 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 744 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: B 744 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6299 (tt0) REVERT: B 1011 MET cc_start: 0.8263 (ppp) cc_final: 0.7805 (ppp) REVERT: B 1014 CYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7229 (m) REVERT: C 918 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7972 (pp20) REVERT: C 976 ASP cc_start: 0.7409 (m-30) cc_final: 0.7052 (m-30) REVERT: C 1011 MET cc_start: 0.8510 (ppp) cc_final: 0.8128 (ppp) outliers start: 39 outliers final: 28 residues processed: 126 average time/residue: 0.2039 time to fit residues: 35.5765 Evaluate side-chains 126 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 986 LEU 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 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 948 LEU Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 0.0980 chunk 88 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 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 = 0.3585 r_free = 0.3585 target = 0.072123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.062421 restraints weight = 37902.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.063970 restraints weight = 23878.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.065044 restraints weight = 17048.526| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5783 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= 0.205 Angle : 0.716 15.080 11448 Z= 0.351 Chirality : 0.051 0.305 1419 Planarity : 0.005 0.046 1461 Dihedral : 10.641 70.414 1590 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.88 % Allowed : 21.26 % Favored : 74.86 % 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: -1.46 (0.25), residues: 1020 helix: 1.55 (0.22), residues: 498 sheet: -2.93 (0.37), residues: 156 loop : -3.79 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1084 HIS 0.003 0.001 HIS B1046 PHE 0.013 0.002 PHE B 741 TYR 0.016 0.001 TYR B 738 ARG 0.009 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 136 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.870 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 744 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6449 (tt0) REVERT: A 936 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7730 (tm-30) REVERT: A 982 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8171 (mtp85) REVERT: B 744 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6291 (tt0) REVERT: B 1011 MET cc_start: 0.8274 (ppp) cc_final: 0.7774 (ppp) REVERT: B 1014 CYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7241 (m) REVERT: C 918 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8007 (pp20) REVERT: C 976 ASP cc_start: 0.7394 (m-30) cc_final: 0.7025 (m-30) REVERT: C 1011 MET cc_start: 0.8501 (ppp) cc_final: 0.8115 (ppp) outliers start: 35 outliers final: 26 residues processed: 126 average time/residue: 0.2021 time to fit residues: 34.7654 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 : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 986 LEU 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 978 LEU Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1126 GLU Chi-restraints excluded: chain C residue 918 GLU 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 994 LEU Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN ** C 942 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.069841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060211 restraints weight = 38479.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.061760 restraints weight = 23881.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062842 restraints weight = 16908.189| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8433 Z= 0.305 Angle : 0.770 14.633 11448 Z= 0.383 Chirality : 0.052 0.278 1419 Planarity : 0.005 0.052 1461 Dihedral : 10.588 66.899 1590 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.99 % Allowed : 21.59 % Favored : 74.42 % 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: 1.37 (0.21), residues: 498 sheet: -2.63 (0.36), residues: 156 loop : -3.77 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C1084 HIS 0.006 0.001 HIS C1030 PHE 0.015 0.002 PHE B 909 TYR 0.013 0.001 TYR B1120 ARG 0.014 0.001 ARG C 977 =============================================================================== Job complete usr+sys time: 2487.74 seconds wall clock time: 44 minutes 46.88 seconds (2686.88 seconds total)