Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 18:22:02 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/12_2021/6m3w_30072.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/12_2021/6m3w_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/12_2021/6m3w_30072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/12_2021/6m3w_30072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/12_2021/6m3w_30072.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m3w_30072/12_2021/6m3w_30072.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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 chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.77, per 1000 atoms: 0.57 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 - 3.50 Amimo acid : False - 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: 3.37 Conformation dependent library (CDL) restraints added in 1.2 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: 0.33 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: 2.13 Time building geometry restraints manager: 3.62 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 1.426 1.518 -0.092 3.20e-02 9.77e+02 8.23e+00 bond pdb=" C1 NAG A1202 " pdb=" O5 NAG A1202 " ideal model delta sigma weight residual 1.426 1.516 -0.090 3.20e-02 9.77e+02 7.95e+00 bond pdb=" C1 NAG B1202 " pdb=" O5 NAG B1202 " ideal model delta sigma weight residual 1.426 1.515 -0.089 3.20e-02 9.77e+02 7.74e+00 bond pdb=" C1 NAG A1205 " pdb=" C2 NAG A1205 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" C1 NAG B1205 " pdb=" C2 NAG B1205 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.60e+00 ... (remaining 8428 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.91: 165 105.91 - 112.96: 4760 112.96 - 120.00: 2915 120.00 - 127.04: 3556 127.04 - 134.08: 52 Bond angle restraints: 11448 Sorted by residual: angle pdb=" C2 NAG C1205 " pdb=" N2 NAG C1205 " pdb=" C7 NAG C1205 " ideal model delta sigma weight residual 123.12 133.62 -10.50 1.28e+00 6.08e-01 6.70e+01 angle pdb=" C2 NAG B1205 " pdb=" N2 NAG B1205 " pdb=" C7 NAG B1205 " ideal model delta sigma weight residual 123.12 133.57 -10.45 1.28e+00 6.08e-01 6.63e+01 angle pdb=" C2 NAG A1205 " pdb=" N2 NAG A1205 " pdb=" C7 NAG A1205 " ideal model delta sigma weight residual 123.12 133.54 -10.42 1.28e+00 6.08e-01 6.59e+01 angle pdb=" C1 NAG B1205 " pdb=" C2 NAG B1205 " pdb=" C3 NAG B1205 " ideal model delta sigma weight residual 110.19 114.65 -4.46 9.25e-01 1.17e+00 2.32e+01 angle pdb=" C1 NAG A1205 " pdb=" C2 NAG A1205 " pdb=" C3 NAG A1205 " ideal model delta sigma weight residual 110.19 114.59 -4.40 9.25e-01 1.17e+00 2.26e+01 ... (remaining 11443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 4842 21.29 - 42.58: 189 42.58 - 63.87: 12 63.87 - 85.17: 27 85.17 - 106.46: 15 Dihedral angle restraints: 5085 sinusoidal: 2070 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 5082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1262 0.110 - 0.220: 139 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 2.440 nonbonded pdb=" O GLY C1149 " pdb=" OG SER C1152 " model vdw 2.264 2.440 nonbonded pdb=" O GLY A1149 " pdb=" OG SER A1152 " model vdw 2.264 2.440 nonbonded pdb=" OD2 ASP A1145 " pdb=" OG SER C 956 " model vdw 2.286 2.440 nonbonded pdb=" O GLU B 918 " pdb=" OG1 THR B 922 " model vdw 2.293 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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 Write .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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.320 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 23.680 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.070 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 38.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 0.092 8433 Z= 0.702 Angle : 1.286 10.504 11448 Z= 0.735 Chirality : 0.077 0.551 1419 Planarity : 0.009 0.073 1461 Dihedral : 14.997 106.457 3087 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 % 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 227 time to evaluate : 1.055 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 outliers start: 6 outliers final: 0 residues processed: 233 average time/residue: 0.2270 time to fit residues: 69.3913 Evaluate side-chains 120 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2747 ------------------------------------------------------------------------------- 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: 5.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 992 GLN A1036 GLN A1090 ASN ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN B1065 HIS C 744 GLN C 993 GLN C1090 ASN C1141 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 8433 Z= 0.267 Angle : 0.741 8.810 11448 Z= 0.412 Chirality : 0.056 0.401 1419 Planarity : 0.005 0.057 1461 Dihedral : 17.672 107.634 1230 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 4.10 % 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: -2.62 (0.24), residues: 1020 helix: 0.10 (0.21), residues: 492 sheet: -3.19 (0.43), residues: 117 loop : -3.68 (0.24), residues: 411 *********************** 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 197 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 1.013 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 outliers start: 37 outliers final: 18 residues processed: 184 average time/residue: 0.2158 time to fit residues: 53.3062 Evaluate side-chains 142 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 0.976 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.0992 time to fit residues: 4.3181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN B1141 HIS C 746 ASN ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 8433 Z= 0.336 Angle : 0.743 10.433 11448 Z= 0.411 Chirality : 0.055 0.334 1419 Planarity : 0.005 0.048 1461 Dihedral : 17.517 107.496 1230 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer Outliers : 3.21 % 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: -2.27 (0.24), residues: 1020 helix: 0.48 (0.21), residues: 495 sheet: -3.15 (0.42), residues: 117 loop : -3.63 (0.24), residues: 408 *********************** 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 145 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.977 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 outliers start: 29 outliers final: 14 residues processed: 138 average time/residue: 0.2242 time to fit residues: 41.6069 Evaluate side-chains 111 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.040 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.0976 time to fit residues: 3.6967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 26 optimal weight: 0.0030 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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** A1141 HIS ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 8433 Z= 0.254 Angle : 0.665 8.567 11448 Z= 0.372 Chirality : 0.052 0.302 1419 Planarity : 0.005 0.047 1461 Dihedral : 17.452 108.271 1230 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer Outliers : 2.66 % 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: -1.87 (0.25), residues: 1020 helix: 0.96 (0.22), residues: 492 sheet: -2.98 (0.40), residues: 126 loop : -3.62 (0.24), residues: 402 *********************** 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 145 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.031 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 outliers start: 24 outliers final: 10 residues processed: 137 average time/residue: 0.2365 time to fit residues: 43.2726 Evaluate side-chains 121 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.962 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.0779 time to fit residues: 2.7361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 8433 Z= 0.343 Angle : 0.705 8.779 11448 Z= 0.395 Chirality : 0.052 0.312 1419 Planarity : 0.005 0.055 1461 Dihedral : 17.518 108.709 1230 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer Outliers : 2.55 % 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: -2.16 (0.24), residues: 1020 helix: 0.91 (0.21), residues: 498 sheet: -3.31 (0.34), residues: 162 loop : -3.99 (0.24), residues: 360 *********************** 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 130 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.993 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 outliers start: 23 outliers final: 14 residues processed: 123 average time/residue: 0.2224 time to fit residues: 37.2507 Evaluate side-chains 115 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.979 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.0825 time to fit residues: 3.3824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 8433 Z= 0.244 Angle : 0.654 10.976 11448 Z= 0.364 Chirality : 0.051 0.275 1419 Planarity : 0.005 0.050 1461 Dihedral : 17.411 108.790 1230 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer Outliers : 1.66 % 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: 498 sheet: -2.68 (0.40), residues: 132 loop : -3.93 (0.22), residues: 390 *********************** 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 130 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.838 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 outliers start: 15 outliers final: 8 residues processed: 126 average time/residue: 0.2099 time to fit residues: 36.1607 Evaluate side-chains 110 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.003 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.1202 time to fit residues: 2.8364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1160 ASN ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.053 8433 Z= 0.530 Angle : 0.873 10.846 11448 Z= 0.479 Chirality : 0.056 0.345 1419 Planarity : 0.006 0.055 1461 Dihedral : 17.701 109.002 1230 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer Outliers : 3.21 % 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: -2.52 (0.23), residues: 1020 helix: 0.47 (0.21), residues: 498 sheet: -3.13 (0.38), residues: 111 loop : -4.12 (0.21), residues: 411 *********************** 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 125 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 0.988 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 outliers start: 29 outliers final: 20 residues processed: 114 average time/residue: 0.2303 time to fit residues: 35.9166 Evaluate side-chains 104 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.014 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.0871 time to fit residues: 4.4591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 8433 Z= 0.256 Angle : 0.707 12.422 11448 Z= 0.386 Chirality : 0.052 0.269 1419 Planarity : 0.005 0.053 1461 Dihedral : 17.490 108.634 1230 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer Outliers : 1.55 % 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: -2.01 (0.24), residues: 1020 helix: 1.03 (0.22), residues: 498 sheet: -3.09 (0.36), residues: 156 loop : -4.00 (0.22), residues: 366 *********************** 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 124 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.973 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 outliers start: 14 outliers final: 4 residues processed: 123 average time/residue: 0.2108 time to fit residues: 35.7272 Evaluate side-chains 98 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.056 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.0848 time to fit residues: 1.9608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN ** 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 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 8433 Z= 0.267 Angle : 0.708 12.675 11448 Z= 0.385 Chirality : 0.051 0.275 1419 Planarity : 0.005 0.050 1461 Dihedral : 17.426 108.279 1230 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer Outliers : 1.77 % 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: -1.89 (0.25), residues: 1020 helix: 1.10 (0.22), residues: 498 sheet: -3.00 (0.36), residues: 156 loop : -3.93 (0.23), residues: 366 *********************** 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 119 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 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 outliers start: 16 outliers final: 11 residues processed: 110 average time/residue: 0.2303 time to fit residues: 34.2309 Evaluate side-chains 105 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.986 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.0816 time to fit residues: 2.9287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN ** B1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 8433 Z= 0.320 Angle : 0.739 13.665 11448 Z= 0.401 Chirality : 0.052 0.288 1419 Planarity : 0.005 0.049 1461 Dihedral : 17.457 108.156 1230 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.98 (0.25), residues: 1020 helix: 1.02 (0.22), residues: 498 sheet: -2.86 (0.33), residues: 192 loop : -4.07 (0.24), residues: 330 ********************** 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 104 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.039 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 outliers start: 10 outliers final: 5 residues processed: 99 average time/residue: 0.2489 time to fit residues: 32.8728 Evaluate side-chains 96 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.017 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.0853 time to fit residues: 2.0220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 ASN ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.072375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.062249 restraints weight = 39542.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063752 restraints weight = 25279.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.064787 restraints weight = 18402.092| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 8433 Z= 0.258 Angle : 0.708 14.324 11448 Z= 0.383 Chirality : 0.051 0.261 1419 Planarity : 0.005 0.049 1461 Dihedral : 17.380 108.176 1230 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 0.33 % 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: -1.83 (0.25), residues: 1020 helix: 1.13 (0.22), residues: 498 sheet: -2.67 (0.34), residues: 192 loop : -4.06 (0.24), residues: 330 =============================================================================== Job complete usr+sys time: 1680.05 seconds wall clock time: 31 minutes 49.34 seconds (1909.34 seconds total)