Starting phenix.real_space_refine on Wed Feb 4 04:29:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9me4_48183/02_2026/9me4_48183.cif Found real_map, /net/cci-nas-00/data/ceres_data/9me4_48183/02_2026/9me4_48183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9me4_48183/02_2026/9me4_48183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9me4_48183/02_2026/9me4_48183.map" model { file = "/net/cci-nas-00/data/ceres_data/9me4_48183/02_2026/9me4_48183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9me4_48183/02_2026/9me4_48183.cif" } resolution = 3.2 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.180 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 36 5.16 5 C 5378 2.51 5 N 1419 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8583 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2052 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 262} Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "H" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1623 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 200} Chain: "I" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1586 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 194} Chain: "L" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1649 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "M" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1528 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 189} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.48, per 1000 atoms: 0.17 Number of scatterers: 8583 At special positions: 0 Unit cell: (66.316, 118.02, 176.468, 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 36 16.00 O 1750 8.00 N 1419 7.00 C 5378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 44 " distance=2.04 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 199 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " 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 ALPHA1-3 " MAN B 3 " - " MAN B 4 " ALPHA1-4 " NAG B 2 " - " MAN B 3 " ALPHA1-6 " MAN B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN L 90 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 286.8 milliseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 30 sheets defined 5.2% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 66 through 69 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.537A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.847A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 190 through 192 No H-bonds generated for 'chain 'I' and resid 190 through 192' Processing helix chain 'L' and resid 120 through 126 Processing helix chain 'L' and resid 181 through 187 removed outlier: 3.631A pdb=" N ARG L 187 " --> pdb=" O ASP L 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 182 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.594A pdb=" N CYS A 3 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.625A pdb=" N GLY A 16 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASN A 147 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 18 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N TYR A 149 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 20 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 127 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA A 150 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 125 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.625A pdb=" N GLY A 16 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASN A 147 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 18 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N TYR A 149 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 20 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 127 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA A 150 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 125 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 54 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 37 removed outlier: 7.010A pdb=" N LEU A 107 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 80 " --> pdb=" O TYR A 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 120 Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 171 removed outlier: 6.616A pdb=" N VAL A 168 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASN G 8 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A 170 " --> pdb=" O ASN G 8 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N LYS G 10 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLN A 191 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA A 242 " --> pdb=" O GLN A 191 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU A 193 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 178 through 180 removed outlier: 3.953A pdb=" N ALA A 257 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.619A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N MET H 34 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.619A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.987A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL H 186 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER H 184 " --> pdb=" O CYS H 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.987A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR H 180 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 156 through 159 Processing sheet with id=AB6, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.519A pdb=" N THR I 71 " --> pdb=" O TYR I 80 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.628A pdb=" N SER I 99 " --> pdb=" O TYR I 33 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR I 33 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.902A pdb=" N CYS I 96 " --> pdb=" O TRP I 107 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TRP I 107 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG I 98 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 124 through 128 removed outlier: 3.512A pdb=" N LYS I 147 " --> pdb=" O SER I 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY I 143 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR I 179 " --> pdb=" O GLY I 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 124 through 128 removed outlier: 3.512A pdb=" N LYS I 147 " --> pdb=" O SER I 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY I 143 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR I 179 " --> pdb=" O GLY I 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 155 through 158 Processing sheet with id=AC3, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.387A pdb=" N VAL L 32 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR L 48 " --> pdb=" O VAL L 32 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP L 34 " --> pdb=" O MET L 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AC6, first strand: chain 'L' and resid 113 through 117 removed outlier: 3.573A pdb=" N ASN L 136 " --> pdb=" O THR L 113 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA L 129 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 152 through 154 removed outlier: 4.321A pdb=" N TRP L 147 " --> pdb=" O ARG L 154 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.719A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.719A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 114 through 117 removed outlier: 3.928A pdb=" N ASN M 137 " --> pdb=" O THR M 114 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 153 through 155 removed outlier: 4.333A pdb=" N TRP M 148 " --> pdb=" O ARG M 155 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.77 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: 2743 1.34 - 1.46: 2181 1.46 - 1.58: 3808 1.58 - 1.70: 1 1.70 - 1.82: 51 Bond restraints: 8784 Sorted by residual: bond pdb=" N THR M 51 " pdb=" CA THR M 51 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.39e+00 bond pdb=" C1 MAN B 3 " pdb=" C2 MAN B 3 " ideal model delta sigma weight residual 1.526 1.585 -0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" N SER A 69 " pdb=" CA SER A 69 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.47e+00 bond pdb=" N VAL H 188 " pdb=" CA VAL H 188 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.23e-02 6.61e+03 7.99e+00 bond pdb=" N THR H 187 " pdb=" CA THR H 187 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.81e+00 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 11627 1.60 - 3.20: 316 3.20 - 4.81: 36 4.81 - 6.41: 5 6.41 - 8.01: 6 Bond angle restraints: 11990 Sorted by residual: angle pdb=" C THR H 187 " pdb=" CA THR H 187 " pdb=" CB THR H 187 " ideal model delta sigma weight residual 109.35 115.32 -5.97 1.98e+00 2.55e-01 9.10e+00 angle pdb=" N GLY H 99 " pdb=" CA GLY H 99 " pdb=" C GLY H 99 " ideal model delta sigma weight residual 113.18 120.02 -6.84 2.37e+00 1.78e-01 8.34e+00 angle pdb=" CA GLU H 196 " pdb=" C GLU H 196 " pdb=" O GLU H 196 " ideal model delta sigma weight residual 121.49 118.32 3.17 1.16e+00 7.43e-01 7.47e+00 angle pdb=" N GLY H 144 " pdb=" CA GLY H 144 " pdb=" C GLY H 144 " ideal model delta sigma weight residual 110.91 114.96 -4.05 1.49e+00 4.50e-01 7.40e+00 angle pdb=" C3 MAN B 4 " pdb=" C2 MAN B 4 " pdb=" O2 MAN B 4 " ideal model delta sigma weight residual 111.77 103.76 8.01 3.00e+00 1.11e-01 7.13e+00 ... (remaining 11985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4712 17.97 - 35.94: 424 35.94 - 53.90: 96 53.90 - 71.87: 23 71.87 - 89.84: 15 Dihedral angle restraints: 5270 sinusoidal: 2024 harmonic: 3246 Sorted by residual: dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " pdb=" CB CYS I 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.90 39.10 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA TYR A 95 " pdb=" C TYR A 95 " pdb=" N ASN A 96 " pdb=" CA ASN A 96 " ideal model delta harmonic sigma weight residual 180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA SER H 30 " pdb=" C SER H 30 " pdb=" N SER H 31 " pdb=" CA SER H 31 " ideal model delta harmonic sigma weight residual -180.00 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1051 0.047 - 0.093: 224 0.093 - 0.140: 94 0.140 - 0.187: 4 0.187 - 0.234: 3 Chirality restraints: 1376 Sorted by residual: chirality pdb=" C4 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C5 NAG B 2 " pdb=" O4 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.30 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN L 90 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA THR M 51 " pdb=" N THR M 51 " pdb=" C THR M 51 " pdb=" CB THR M 51 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1373 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 139 " 0.040 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO L 140 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO L 140 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 140 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 193 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO H 194 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO H 194 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 194 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 152 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO I 153 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO I 153 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 153 " -0.022 5.00e-02 4.00e+02 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 948 2.75 - 3.28: 7746 3.28 - 3.82: 13533 3.82 - 4.36: 15935 4.36 - 4.90: 29094 Nonbonded interactions: 67256 Sorted by model distance: nonbonded pdb=" OG1 THR I 136 " pdb=" O MET I 139 " model vdw 2.208 3.040 nonbonded pdb=" NZ LYS A 76 " pdb=" OD1 ASP I 52 " model vdw 2.212 3.120 nonbonded pdb=" OG SER I 116 " pdb=" OD1 ASP I 177 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASN M 138 " pdb=" OG1 THR M 172 " model vdw 2.246 3.040 nonbonded pdb=" NH1 ARG M 24 " pdb=" OD1 ASP M 70 " model vdw 2.248 3.120 ... (remaining 67251 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 6.210 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.005 0.059 8799 Z= 0.231 Angle : 0.654 10.449 12025 Z= 0.345 Chirality : 0.046 0.234 1376 Planarity : 0.005 0.059 1536 Dihedral : 15.317 89.841 3172 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.83 % Allowed : 17.24 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1112 helix: 0.16 (1.02), residues: 29 sheet: 0.64 (0.24), residues: 497 loop : -0.66 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 43 TYR 0.016 0.002 TYR A 95 PHE 0.013 0.002 PHE A 84 TRP 0.012 0.002 TRP I 47 HIS 0.006 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 8784) covalent geometry : angle 0.63886 (11990) SS BOND : bond 0.00367 ( 10) SS BOND : angle 1.56226 ( 20) hydrogen bonds : bond 0.24409 ( 320) hydrogen bonds : angle 9.42892 ( 867) link_ALPHA1-3 : bond 0.00793 ( 1) link_ALPHA1-3 : angle 2.96600 ( 3) link_ALPHA1-4 : bond 0.00467 ( 1) link_ALPHA1-4 : angle 6.17830 ( 3) link_ALPHA1-6 : bond 0.01202 ( 1) link_ALPHA1-6 : angle 1.08834 ( 3) link_BETA1-4 : bond 0.00037 ( 1) link_BETA1-4 : angle 4.42969 ( 3) link_NAG-ASN : bond 0.00003 ( 1) link_NAG-ASN : angle 1.09259 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.293 Fit side-chains REVERT: I 119 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7719 (mmtp) outliers start: 8 outliers final: 3 residues processed: 149 average time/residue: 0.0745 time to fit residues: 15.6580 Evaluate side-chains 138 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain M residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.4980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 45 HIS A 59 GLN A 152 ASN A 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.170173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.106894 restraints weight = 9813.435| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.23 r_work: 0.2900 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8799 Z= 0.159 Angle : 0.621 8.516 12025 Z= 0.321 Chirality : 0.047 0.245 1376 Planarity : 0.005 0.055 1536 Dihedral : 6.753 59.735 1318 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.01 % Allowed : 16.10 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.25), residues: 1112 helix: 0.17 (1.01), residues: 30 sheet: 0.78 (0.23), residues: 505 loop : -0.62 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.016 0.002 TYR A 95 PHE 0.012 0.001 PHE L 208 TRP 0.010 0.002 TRP I 47 HIS 0.005 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8784) covalent geometry : angle 0.60921 (11990) SS BOND : bond 0.00570 ( 10) SS BOND : angle 1.27140 ( 20) hydrogen bonds : bond 0.03903 ( 320) hydrogen bonds : angle 6.44264 ( 867) link_ALPHA1-3 : bond 0.00957 ( 1) link_ALPHA1-3 : angle 2.13825 ( 3) link_ALPHA1-4 : bond 0.00967 ( 1) link_ALPHA1-4 : angle 5.12140 ( 3) link_ALPHA1-6 : bond 0.01326 ( 1) link_ALPHA1-6 : angle 1.31589 ( 3) link_BETA1-4 : bond 0.00588 ( 1) link_BETA1-4 : angle 4.01308 ( 3) link_NAG-ASN : bond 0.00410 ( 1) link_NAG-ASN : angle 1.72774 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.268 Fit side-chains REVERT: H 63 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7929 (ptmm) REVERT: H 74 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7839 (mtmt) REVERT: M 72 SER cc_start: 0.8761 (p) cc_final: 0.8505 (m) outliers start: 29 outliers final: 19 residues processed: 162 average time/residue: 0.0823 time to fit residues: 18.7249 Evaluate side-chains 163 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.0000 chunk 61 optimal weight: 0.4980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN I 39 GLN M 38 GLN M 138 ASN M 161 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.168605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.105620 restraints weight = 9786.177| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.28 r_work: 0.2876 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8799 Z= 0.218 Angle : 0.646 8.806 12025 Z= 0.331 Chirality : 0.048 0.260 1376 Planarity : 0.005 0.056 1536 Dihedral : 6.504 59.032 1314 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.57 % Allowed : 15.37 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.25), residues: 1112 helix: 0.26 (1.03), residues: 30 sheet: 0.93 (0.23), residues: 504 loop : -0.68 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 43 TYR 0.018 0.002 TYR A 95 PHE 0.014 0.002 PHE H 95 TRP 0.012 0.002 TRP I 36 HIS 0.005 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 8784) covalent geometry : angle 0.63432 (11990) SS BOND : bond 0.00583 ( 10) SS BOND : angle 1.46772 ( 20) hydrogen bonds : bond 0.03912 ( 320) hydrogen bonds : angle 6.05438 ( 867) link_ALPHA1-3 : bond 0.00942 ( 1) link_ALPHA1-3 : angle 2.14372 ( 3) link_ALPHA1-4 : bond 0.00894 ( 1) link_ALPHA1-4 : angle 5.22563 ( 3) link_ALPHA1-6 : bond 0.01482 ( 1) link_ALPHA1-6 : angle 1.31062 ( 3) link_BETA1-4 : bond 0.00226 ( 1) link_BETA1-4 : angle 3.78336 ( 3) link_NAG-ASN : bond 0.00291 ( 1) link_NAG-ASN : angle 1.63905 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.315 Fit side-chains REVERT: A 252 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8206 (mt) REVERT: H 5 GLN cc_start: 0.7985 (tp40) cc_final: 0.7658 (mm-40) REVERT: H 63 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8007 (ptmm) REVERT: H 74 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7754 (mtmt) outliers start: 44 outliers final: 33 residues processed: 174 average time/residue: 0.0738 time to fit residues: 18.3028 Evaluate side-chains 179 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 107 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 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 23 ASN A 267 ASN L 6 GLN M 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.168120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.105576 restraints weight = 9906.116| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.10 r_work: 0.2868 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 8799 Z= 0.249 Angle : 0.667 9.414 12025 Z= 0.341 Chirality : 0.048 0.267 1376 Planarity : 0.005 0.055 1536 Dihedral : 6.524 57.448 1314 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.88 % Allowed : 15.89 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 1112 helix: 0.40 (1.06), residues: 30 sheet: 0.94 (0.23), residues: 504 loop : -0.74 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 43 TYR 0.019 0.002 TYR A 95 PHE 0.015 0.002 PHE H 95 TRP 0.013 0.002 TRP I 36 HIS 0.005 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 8784) covalent geometry : angle 0.65512 (11990) SS BOND : bond 0.00619 ( 10) SS BOND : angle 1.50875 ( 20) hydrogen bonds : bond 0.03754 ( 320) hydrogen bonds : angle 5.91052 ( 867) link_ALPHA1-3 : bond 0.00872 ( 1) link_ALPHA1-3 : angle 1.96478 ( 3) link_ALPHA1-4 : bond 0.00751 ( 1) link_ALPHA1-4 : angle 5.46306 ( 3) link_ALPHA1-6 : bond 0.01382 ( 1) link_ALPHA1-6 : angle 1.19949 ( 3) link_BETA1-4 : bond 0.00210 ( 1) link_BETA1-4 : angle 3.83016 ( 3) link_NAG-ASN : bond 0.00169 ( 1) link_NAG-ASN : angle 1.47851 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 0.270 Fit side-chains REVERT: A 252 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8251 (mt) REVERT: H 5 GLN cc_start: 0.8027 (tp40) cc_final: 0.7676 (mm-40) REVERT: H 63 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8052 (ptmm) REVERT: H 74 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7787 (mtmt) REVERT: I 73 ASP cc_start: 0.8894 (t70) cc_final: 0.8667 (t70) REVERT: I 109 GLN cc_start: 0.9377 (OUTLIER) cc_final: 0.8480 (pm20) outliers start: 47 outliers final: 38 residues processed: 174 average time/residue: 0.0761 time to fit residues: 18.8753 Evaluate side-chains 184 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 172 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 84 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 73 optimal weight: 0.0980 chunk 52 optimal weight: 0.0970 chunk 100 optimal weight: 0.5980 chunk 66 optimal weight: 0.0980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN M 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.169580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.106523 restraints weight = 9929.559| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.26 r_work: 0.2904 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8799 Z= 0.140 Angle : 0.583 8.521 12025 Z= 0.296 Chirality : 0.046 0.242 1376 Planarity : 0.004 0.056 1536 Dihedral : 6.139 57.353 1314 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.84 % Allowed : 16.82 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1112 helix: 0.32 (1.05), residues: 30 sheet: 1.06 (0.23), residues: 506 loop : -0.64 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 43 TYR 0.013 0.001 TYR A 95 PHE 0.013 0.001 PHE H 95 TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8784) covalent geometry : angle 0.57287 (11990) SS BOND : bond 0.00448 ( 10) SS BOND : angle 1.04168 ( 20) hydrogen bonds : bond 0.03036 ( 320) hydrogen bonds : angle 5.53264 ( 867) link_ALPHA1-3 : bond 0.01019 ( 1) link_ALPHA1-3 : angle 1.82683 ( 3) link_ALPHA1-4 : bond 0.01034 ( 1) link_ALPHA1-4 : angle 5.03003 ( 3) link_ALPHA1-6 : bond 0.01490 ( 1) link_ALPHA1-6 : angle 1.28299 ( 3) link_BETA1-4 : bond 0.00478 ( 1) link_BETA1-4 : angle 3.57546 ( 3) link_NAG-ASN : bond 0.00358 ( 1) link_NAG-ASN : angle 1.55984 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.293 Fit side-chains REVERT: A 239 SER cc_start: 0.7584 (t) cc_final: 0.6993 (m) REVERT: A 252 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8203 (mt) REVERT: H 5 GLN cc_start: 0.7985 (tp40) cc_final: 0.7664 (mm-40) REVERT: H 63 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7993 (ptmm) REVERT: H 74 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7750 (mtmt) REVERT: H 110 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7447 (pm20) REVERT: I 73 ASP cc_start: 0.8862 (t70) cc_final: 0.8599 (t70) REVERT: I 109 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8463 (pm20) outliers start: 37 outliers final: 28 residues processed: 170 average time/residue: 0.0713 time to fit residues: 17.3815 Evaluate side-chains 179 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 56 optimal weight: 0.0670 chunk 98 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN I 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.169324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.106367 restraints weight = 9856.522| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.17 r_work: 0.2903 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8799 Z= 0.155 Angle : 0.589 9.426 12025 Z= 0.299 Chirality : 0.046 0.237 1376 Planarity : 0.005 0.057 1536 Dihedral : 6.060 57.538 1314 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.67 % Allowed : 17.13 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1112 helix: 0.43 (1.08), residues: 30 sheet: 1.15 (0.23), residues: 504 loop : -0.67 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 43 TYR 0.015 0.001 TYR A 95 PHE 0.013 0.001 PHE H 95 TRP 0.010 0.001 TRP I 47 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8784) covalent geometry : angle 0.57875 (11990) SS BOND : bond 0.00487 ( 10) SS BOND : angle 1.09144 ( 20) hydrogen bonds : bond 0.03077 ( 320) hydrogen bonds : angle 5.39229 ( 867) link_ALPHA1-3 : bond 0.01039 ( 1) link_ALPHA1-3 : angle 1.74475 ( 3) link_ALPHA1-4 : bond 0.00923 ( 1) link_ALPHA1-4 : angle 4.81325 ( 3) link_ALPHA1-6 : bond 0.01474 ( 1) link_ALPHA1-6 : angle 1.27453 ( 3) link_BETA1-4 : bond 0.00326 ( 1) link_BETA1-4 : angle 3.62304 ( 3) link_NAG-ASN : bond 0.00283 ( 1) link_NAG-ASN : angle 1.38954 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.229 Fit side-chains REVERT: A 156 VAL cc_start: 0.8720 (t) cc_final: 0.8503 (m) REVERT: A 239 SER cc_start: 0.7581 (t) cc_final: 0.7001 (m) REVERT: A 252 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8218 (mt) REVERT: H 5 GLN cc_start: 0.7888 (tp40) cc_final: 0.7552 (mm-40) REVERT: H 63 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8021 (ptmm) REVERT: H 74 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7750 (mtmt) REVERT: H 81 MET cc_start: 0.8669 (ttt) cc_final: 0.8171 (ttp) REVERT: H 110 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8280 (pm20) REVERT: I 73 ASP cc_start: 0.8857 (t70) cc_final: 0.8564 (t70) REVERT: I 109 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8470 (pm20) REVERT: M 73 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8884 (tp) outliers start: 45 outliers final: 37 residues processed: 178 average time/residue: 0.0740 time to fit residues: 18.6725 Evaluate side-chains 192 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 0.0970 chunk 96 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 267 ASN M 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.166924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.103531 restraints weight = 9944.742| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.13 r_work: 0.2868 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 8799 Z= 0.263 Angle : 0.672 10.305 12025 Z= 0.341 Chirality : 0.048 0.268 1376 Planarity : 0.005 0.057 1536 Dihedral : 6.419 56.984 1314 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.92 % Allowed : 16.51 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1112 helix: 0.50 (1.10), residues: 30 sheet: 1.02 (0.23), residues: 492 loop : -0.79 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 43 TYR 0.022 0.002 TYR A 95 PHE 0.016 0.002 PHE L 86 TRP 0.014 0.002 TRP I 36 HIS 0.004 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 8784) covalent geometry : angle 0.66082 (11990) SS BOND : bond 0.00615 ( 10) SS BOND : angle 1.47068 ( 20) hydrogen bonds : bond 0.03625 ( 320) hydrogen bonds : angle 5.64408 ( 867) link_ALPHA1-3 : bond 0.00792 ( 1) link_ALPHA1-3 : angle 1.76640 ( 3) link_ALPHA1-4 : bond 0.00754 ( 1) link_ALPHA1-4 : angle 5.39784 ( 3) link_ALPHA1-6 : bond 0.01359 ( 1) link_ALPHA1-6 : angle 1.13439 ( 3) link_BETA1-4 : bond 0.00140 ( 1) link_BETA1-4 : angle 3.76709 ( 3) link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 1.29259 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 149 time to evaluate : 0.315 Fit side-chains REVERT: A 60 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7860 (ttm-80) REVERT: H 5 GLN cc_start: 0.8036 (tp40) cc_final: 0.7695 (mm-40) REVERT: H 63 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8115 (ptmm) REVERT: I 73 ASP cc_start: 0.8885 (t70) cc_final: 0.8568 (t70) REVERT: I 109 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: L 46 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8513 (mmt) REVERT: M 73 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8911 (tp) outliers start: 57 outliers final: 48 residues processed: 181 average time/residue: 0.0703 time to fit residues: 18.1243 Evaluate side-chains 202 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 26 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.0270 chunk 82 optimal weight: 0.5980 chunk 57 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 100 optimal weight: 0.0970 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.170581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.107907 restraints weight = 9821.513| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.31 r_work: 0.2904 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8799 Z= 0.130 Angle : 0.575 10.235 12025 Z= 0.291 Chirality : 0.045 0.233 1376 Planarity : 0.004 0.057 1536 Dihedral : 5.996 57.214 1314 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.57 % Allowed : 17.86 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1112 helix: 0.40 (1.08), residues: 30 sheet: 1.15 (0.23), residues: 501 loop : -0.73 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 43 TYR 0.012 0.001 TYR I 50 PHE 0.012 0.001 PHE H 95 TRP 0.010 0.001 TRP I 47 HIS 0.003 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8784) covalent geometry : angle 0.56510 (11990) SS BOND : bond 0.00398 ( 10) SS BOND : angle 0.98595 ( 20) hydrogen bonds : bond 0.02882 ( 320) hydrogen bonds : angle 5.27426 ( 867) link_ALPHA1-3 : bond 0.01113 ( 1) link_ALPHA1-3 : angle 1.62103 ( 3) link_ALPHA1-4 : bond 0.01031 ( 1) link_ALPHA1-4 : angle 4.90237 ( 3) link_ALPHA1-6 : bond 0.01562 ( 1) link_ALPHA1-6 : angle 1.27121 ( 3) link_BETA1-4 : bond 0.00460 ( 1) link_BETA1-4 : angle 3.57278 ( 3) link_NAG-ASN : bond 0.00386 ( 1) link_NAG-ASN : angle 1.51790 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.200 Fit side-chains REVERT: A 239 SER cc_start: 0.7468 (t) cc_final: 0.6848 (m) REVERT: H 5 GLN cc_start: 0.7984 (tp40) cc_final: 0.7659 (mm-40) REVERT: H 63 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8020 (ptmm) REVERT: H 67 LYS cc_start: 0.7386 (ttmm) cc_final: 0.7012 (ttmm) REVERT: H 74 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7753 (mtmt) REVERT: H 81 MET cc_start: 0.8670 (ttt) cc_final: 0.8174 (ttp) REVERT: H 97 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: I 73 ASP cc_start: 0.8873 (t70) cc_final: 0.8542 (t70) REVERT: I 109 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8486 (pm20) REVERT: L 46 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8554 (mmt) REVERT: M 17 ASP cc_start: 0.7430 (t70) cc_final: 0.7213 (t70) REVERT: M 73 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8870 (tp) outliers start: 44 outliers final: 33 residues processed: 171 average time/residue: 0.0706 time to fit residues: 17.3420 Evaluate side-chains 183 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 10 optimal weight: 0.3980 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 94 optimal weight: 0.2980 chunk 80 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN I 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.168774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.105949 restraints weight = 9784.155| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.22 r_work: 0.2880 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 8799 Z= 0.243 Angle : 0.650 10.712 12025 Z= 0.331 Chirality : 0.048 0.256 1376 Planarity : 0.005 0.057 1536 Dihedral : 6.266 58.333 1314 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.09 % Allowed : 17.55 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.25), residues: 1112 helix: 0.50 (1.10), residues: 30 sheet: 1.09 (0.23), residues: 492 loop : -0.82 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 43 TYR 0.020 0.002 TYR A 95 PHE 0.015 0.002 PHE H 95 TRP 0.013 0.002 TRP I 36 HIS 0.005 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 8784) covalent geometry : angle 0.63897 (11990) SS BOND : bond 0.00557 ( 10) SS BOND : angle 1.46199 ( 20) hydrogen bonds : bond 0.03457 ( 320) hydrogen bonds : angle 5.47048 ( 867) link_ALPHA1-3 : bond 0.00956 ( 1) link_ALPHA1-3 : angle 1.53053 ( 3) link_ALPHA1-4 : bond 0.00706 ( 1) link_ALPHA1-4 : angle 5.16304 ( 3) link_ALPHA1-6 : bond 0.01488 ( 1) link_ALPHA1-6 : angle 1.16204 ( 3) link_BETA1-4 : bond 0.00137 ( 1) link_BETA1-4 : angle 3.69762 ( 3) link_NAG-ASN : bond 0.00160 ( 1) link_NAG-ASN : angle 1.31229 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 0.290 Fit side-chains REVERT: H 5 GLN cc_start: 0.7914 (tp40) cc_final: 0.7600 (mm-40) REVERT: H 63 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8079 (ptmm) REVERT: H 74 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7775 (mtmt) REVERT: H 81 MET cc_start: 0.8766 (ttt) cc_final: 0.8307 (ttp) REVERT: H 97 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: I 73 ASP cc_start: 0.8892 (t70) cc_final: 0.8545 (t70) REVERT: I 109 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8494 (pm20) REVERT: L 46 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8547 (mmt) REVERT: M 73 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8894 (tp) REVERT: M 160 LEU cc_start: 0.8430 (mt) cc_final: 0.8174 (mt) outliers start: 49 outliers final: 39 residues processed: 176 average time/residue: 0.0782 time to fit residues: 19.5818 Evaluate side-chains 191 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.0000 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 54 optimal weight: 0.0970 chunk 33 optimal weight: 0.2980 chunk 103 optimal weight: 0.6980 overall best weight: 0.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.170053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.111059 restraints weight = 9834.181| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.29 r_work: 0.2893 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8799 Z= 0.133 Angle : 0.573 10.470 12025 Z= 0.291 Chirality : 0.045 0.230 1376 Planarity : 0.005 0.056 1536 Dihedral : 5.955 57.683 1314 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.47 % Allowed : 17.96 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1112 helix: 0.40 (1.09), residues: 30 sheet: 1.14 (0.23), residues: 513 loop : -0.74 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 43 TYR 0.012 0.001 TYR I 50 PHE 0.012 0.001 PHE H 95 TRP 0.010 0.001 TRP I 47 HIS 0.004 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8784) covalent geometry : angle 0.56253 (11990) SS BOND : bond 0.00436 ( 10) SS BOND : angle 1.04291 ( 20) hydrogen bonds : bond 0.02883 ( 320) hydrogen bonds : angle 5.20120 ( 867) link_ALPHA1-3 : bond 0.01071 ( 1) link_ALPHA1-3 : angle 1.53743 ( 3) link_ALPHA1-4 : bond 0.00996 ( 1) link_ALPHA1-4 : angle 4.80235 ( 3) link_ALPHA1-6 : bond 0.01529 ( 1) link_ALPHA1-6 : angle 1.28821 ( 3) link_BETA1-4 : bond 0.00441 ( 1) link_BETA1-4 : angle 3.59783 ( 3) link_NAG-ASN : bond 0.00361 ( 1) link_NAG-ASN : angle 1.48547 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.287 Fit side-chains REVERT: A 239 SER cc_start: 0.7449 (t) cc_final: 0.6851 (m) REVERT: H 5 GLN cc_start: 0.7888 (tp40) cc_final: 0.7590 (mm-40) REVERT: H 63 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8048 (ptmm) REVERT: H 74 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7751 (mtmt) REVERT: H 81 MET cc_start: 0.8663 (ttt) cc_final: 0.8217 (ttp) REVERT: H 97 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: I 73 ASP cc_start: 0.8888 (t70) cc_final: 0.8540 (t70) REVERT: I 109 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: L 46 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8589 (mmt) REVERT: M 17 ASP cc_start: 0.7481 (t70) cc_final: 0.7275 (t70) REVERT: M 73 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8878 (tp) REVERT: M 108 ARG cc_start: 0.7732 (ptm160) cc_final: 0.7382 (ptm160) REVERT: M 160 LEU cc_start: 0.8453 (mt) cc_final: 0.8241 (mt) outliers start: 43 outliers final: 35 residues processed: 168 average time/residue: 0.0700 time to fit residues: 16.6626 Evaluate side-chains 185 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.169299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.107106 restraints weight = 9786.281| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.07 r_work: 0.2900 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 8799 Z= 0.228 Angle : 0.638 10.849 12025 Z= 0.325 Chirality : 0.047 0.255 1376 Planarity : 0.005 0.057 1536 Dihedral : 6.186 59.183 1314 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.98 % Allowed : 17.34 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.25), residues: 1112 helix: 0.54 (1.12), residues: 30 sheet: 1.10 (0.23), residues: 511 loop : -0.81 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 43 TYR 0.019 0.002 TYR A 95 PHE 0.015 0.002 PHE H 95 TRP 0.013 0.002 TRP I 36 HIS 0.005 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 8784) covalent geometry : angle 0.62718 (11990) SS BOND : bond 0.00532 ( 10) SS BOND : angle 1.43982 ( 20) hydrogen bonds : bond 0.03391 ( 320) hydrogen bonds : angle 5.39081 ( 867) link_ALPHA1-3 : bond 0.00939 ( 1) link_ALPHA1-3 : angle 1.46725 ( 3) link_ALPHA1-4 : bond 0.00738 ( 1) link_ALPHA1-4 : angle 5.06253 ( 3) link_ALPHA1-6 : bond 0.01490 ( 1) link_ALPHA1-6 : angle 1.17651 ( 3) link_BETA1-4 : bond 0.00171 ( 1) link_BETA1-4 : angle 3.69986 ( 3) link_NAG-ASN : bond 0.00172 ( 1) link_NAG-ASN : angle 1.30546 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2602.86 seconds wall clock time: 45 minutes 11.33 seconds (2711.33 seconds total)