Starting phenix.real_space_refine on Tue Mar 3 14:38:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d72_46600/03_2026/9d72_46600.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d72_46600/03_2026/9d72_46600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d72_46600/03_2026/9d72_46600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d72_46600/03_2026/9d72_46600.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d72_46600/03_2026/9d72_46600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d72_46600/03_2026/9d72_46600.map" } resolution = 2.67 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= 0.001 sd= 0.011 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 29 5.16 5 C 3814 2.51 5 N 1035 2.21 5 O 1162 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6040 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 784 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 88} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1579 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 3, 'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "P" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2096 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 72 Chain: "H" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1505 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 14, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 1.41, per 1000 atoms: 0.23 Number of scatterers: 6040 At special positions: 0 Unit cell: (58.93, 81.34, 138.61, 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 29 16.00 O 1162 8.00 N 1035 7.00 C 3814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 205 " 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 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 258.7 milliseconds 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1476 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 12.4% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.525A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 56 through 85 Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.657A pdb=" N THR A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 3.971A pdb=" N ARG A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N CYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.527A pdb=" N LEU A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 213 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 8 removed outlier: 6.503A pdb=" N PHE B 62 " --> pdb=" O GLN B 29 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR B 63 " --> pdb=" O MET B 54 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET B 54 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU B 65 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 45 removed outlier: 3.888A pdb=" N GLU B 36 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 83 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 6 through 7 removed outlier: 3.595A pdb=" N SER L 7 " --> pdb=" O ASN L 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.079A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 116 through 118 removed outlier: 3.533A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 145 through 146 removed outlier: 3.720A pdb=" N SER L 145 " --> pdb=" O VAL L 197 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL L 197 " --> pdb=" O SER L 145 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.679A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG A 35 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A 101 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 117 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TRP A 114 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N TYR A 118 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASP A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.595A pdb=" N CYS A 203 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 207 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE A 241 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.595A pdb=" N CYS A 203 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 207 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE A 241 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 234 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 214 through 218 removed outlier: 3.544A pdb=" N THR A 214 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS A 259 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 272 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 261 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 5 through 7 removed outlier: 5.361A pdb=" N LYS H 16 " --> pdb=" O SER H 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.549A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 94 " --> pdb=" O GLN H 41 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG H 101 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR H 106 " --> pdb=" O TYR H 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.549A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 94 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.622A pdb=" N LEU H 151 " --> pdb=" O TYR H 132 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU H 134 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR H 185 " --> pdb=" O GLY H 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.622A pdb=" N LEU H 151 " --> pdb=" O TYR H 132 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU H 134 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR H 185 " --> pdb=" O GLY H 154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 161 through 164 263 hydrogen bonds defined for protein. 693 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: 0.99 Time building geometry restraints manager: 0.52 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: 1962 1.34 - 1.46: 1561 1.46 - 1.58: 2632 1.58 - 1.70: 0 1.70 - 1.82: 43 Bond restraints: 6198 Sorted by residual: bond pdb=" N PRO A 184 " pdb=" CA PRO A 184 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.31e-02 5.83e+03 8.74e-01 bond pdb=" CA VAL H 160 " pdb=" CB VAL H 160 " ideal model delta sigma weight residual 1.550 1.541 0.009 1.03e-02 9.43e+03 8.37e-01 bond pdb=" C HIS A 191 " pdb=" N HIS A 192 " ideal model delta sigma weight residual 1.325 1.335 -0.010 1.14e-02 7.69e+03 8.35e-01 bond pdb=" CA LYS B 83 " pdb=" C LYS B 83 " ideal model delta sigma weight residual 1.529 1.521 0.008 1.04e-02 9.25e+03 5.99e-01 bond pdb=" CB THR A 182 " pdb=" CG2 THR A 182 " ideal model delta sigma weight residual 1.521 1.546 -0.025 3.30e-02 9.18e+02 5.66e-01 ... (remaining 6193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 8253 1.40 - 2.81: 160 2.81 - 4.21: 31 4.21 - 5.62: 6 5.62 - 7.02: 2 Bond angle restraints: 8452 Sorted by residual: angle pdb=" C HIS A 192 " pdb=" CA HIS A 192 " pdb=" CB HIS A 192 " ideal model delta sigma weight residual 115.79 110.48 5.31 1.19e+00 7.06e-01 1.99e+01 angle pdb=" N GLY A 107 " pdb=" CA GLY A 107 " pdb=" C GLY A 107 " ideal model delta sigma weight residual 115.63 111.51 4.12 1.49e+00 4.50e-01 7.65e+00 angle pdb=" C LYS B 83 " pdb=" N HIS B 84 " pdb=" CA HIS B 84 " ideal model delta sigma weight residual 121.54 116.35 5.19 1.91e+00 2.74e-01 7.39e+00 angle pdb=" CA LEU A 230 " pdb=" CB LEU A 230 " pdb=" CG LEU A 230 " ideal model delta sigma weight residual 116.30 123.32 -7.02 3.50e+00 8.16e-02 4.02e+00 angle pdb=" C TYR A 85 " pdb=" N ASN A 86 " pdb=" CA ASN A 86 " ideal model delta sigma weight residual 121.54 125.27 -3.73 1.91e+00 2.74e-01 3.82e+00 ... (remaining 8447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.61: 3274 11.61 - 23.22: 264 23.22 - 34.84: 82 34.84 - 46.45: 37 46.45 - 58.06: 13 Dihedral angle restraints: 3670 sinusoidal: 1374 harmonic: 2296 Sorted by residual: dihedral pdb=" CA ALA B 85 " pdb=" C ALA B 85 " pdb=" N SER B 86 " pdb=" CA SER B 86 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" N LEU A 78 " pdb=" CA LEU A 78 " pdb=" CB LEU A 78 " pdb=" CG LEU A 78 " ideal model delta sinusoidal sigma weight residual -60.00 -118.06 58.06 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LEU L 179 " pdb=" CA LEU L 179 " pdb=" CB LEU L 179 " pdb=" CG LEU L 179 " ideal model delta sinusoidal sigma weight residual -60.00 -116.69 56.69 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 615 0.031 - 0.063: 191 0.063 - 0.094: 63 0.094 - 0.126: 55 0.126 - 0.157: 2 Chirality restraints: 926 Sorted by residual: chirality pdb=" CG LEU A 230 " pdb=" CB LEU A 230 " pdb=" CD1 LEU A 230 " pdb=" CD2 LEU A 230 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA TYR L 94 " pdb=" N TYR L 94 " pdb=" C TYR L 94 " pdb=" CB TYR L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA VAL B 9 " pdb=" N VAL B 9 " pdb=" C VAL B 9 " pdb=" CB VAL B 9 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 923 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 94 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO L 95 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 64 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO H 65 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 65 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 65 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 181 " 0.110 9.50e-02 1.11e+02 4.95e-02 1.51e+00 pdb=" NE ARG A 181 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 181 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 181 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 181 " 0.004 2.00e-02 2.50e+03 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 986 2.77 - 3.30: 6031 3.30 - 3.83: 10255 3.83 - 4.37: 11330 4.37 - 4.90: 19679 Nonbonded interactions: 48281 Sorted by model distance: nonbonded pdb=" OH TYR L 94 " pdb=" NH2 ARG H 102 " model vdw 2.234 3.120 nonbonded pdb=" O ILE L 29 " pdb=" OH TYR L 71 " model vdw 2.244 3.040 nonbonded pdb=" NH2 ARG P 5 " pdb=" OD2 ASP A 77 " model vdw 2.245 3.120 nonbonded pdb=" OE1 GLU A 24 " pdb=" OH TYR A 45 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLN A 87 " pdb=" NE2 HIS A 93 " model vdw 2.290 3.120 ... (remaining 48276 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.120 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.002 0.025 6205 Z= 0.123 Angle : 0.521 7.021 8466 Z= 0.275 Chirality : 0.041 0.157 926 Planarity : 0.004 0.050 1090 Dihedral : 11.066 58.060 2173 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.97 % Favored : 93.77 % Rotamer: Outliers : 6.69 % Allowed : 9.87 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -0.24 (0.32), residues: 770 helix: 2.02 (0.60), residues: 80 sheet: 0.17 (0.32), residues: 312 loop : -0.89 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.011 0.001 TYR L 91 PHE 0.007 0.001 PHE A 33 TRP 0.008 0.001 TRP A 114 HIS 0.004 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 6198) covalent geometry : angle 0.52059 ( 8452) SS BOND : bond 0.00322 ( 7) SS BOND : angle 0.75170 ( 14) hydrogen bonds : bond 0.26604 ( 233) hydrogen bonds : angle 9.63895 ( 693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.6900 (ppp) cc_final: 0.6538 (ppp) REVERT: B 52 SER cc_start: 0.7439 (t) cc_final: 0.6196 (p) REVERT: B 54 MET cc_start: 0.7487 (mpp) cc_final: 0.7212 (tpp) REVERT: L 46 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7426 (tp) REVERT: L 137 ASN cc_start: 0.8890 (m-40) cc_final: 0.7988 (m-40) REVERT: H 92 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7965 (t) REVERT: H 163 THR cc_start: 0.8972 (p) cc_final: 0.8771 (t) REVERT: H 174 HIS cc_start: 0.8668 (t-90) cc_final: 0.8181 (t-170) outliers start: 42 outliers final: 11 residues processed: 158 average time/residue: 0.4725 time to fit residues: 78.5046 Evaluate side-chains 82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 179 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 2 GLN B 21 ASN B 24 ASN B 38 GLN L 31 ASN A 42 ASN A 260 HIS A 263 HIS ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN H 206 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.102620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.082415 restraints weight = 21124.566| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 4.87 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6205 Z= 0.149 Angle : 0.690 10.884 8466 Z= 0.347 Chirality : 0.046 0.222 926 Planarity : 0.005 0.052 1090 Dihedral : 5.776 53.516 880 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.27 % Favored : 92.60 % Rotamer: Outliers : 5.10 % Allowed : 16.56 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -0.37 (0.32), residues: 770 helix: 1.50 (0.60), residues: 83 sheet: 0.06 (0.30), residues: 321 loop : -0.89 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 145 TYR 0.018 0.002 TYR L 91 PHE 0.012 0.001 PHE H 176 TRP 0.012 0.001 TRP A 114 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6198) covalent geometry : angle 0.68930 ( 8452) SS BOND : bond 0.00464 ( 7) SS BOND : angle 1.05625 ( 14) hydrogen bonds : bond 0.04622 ( 233) hydrogen bonds : angle 6.85663 ( 693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 SER cc_start: 0.7971 (t) cc_final: 0.6830 (p) REVERT: B 54 MET cc_start: 0.7819 (mpp) cc_final: 0.7399 (tpp) REVERT: B 89 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7461 (mm-30) REVERT: A 45 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: A 70 ASN cc_start: 0.8173 (m-40) cc_final: 0.7879 (m-40) REVERT: A 208 PHE cc_start: 0.6255 (p90) cc_final: 0.5838 (p90) REVERT: H 60 TYR cc_start: 0.7193 (m-80) cc_final: 0.6985 (m-10) REVERT: H 92 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7829 (m) REVERT: H 125 GLU cc_start: 0.8881 (tp30) cc_final: 0.8571 (tm-30) outliers start: 32 outliers final: 14 residues processed: 126 average time/residue: 0.4381 time to fit residues: 58.4794 Evaluate side-chains 93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 175 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 39 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN L 31 ASN A 115 GLN A 176 ASN A 242 GLN ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.097240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.075993 restraints weight = 21243.967| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 4.79 r_work: 0.3635 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 6205 Z= 0.329 Angle : 0.799 9.090 8466 Z= 0.416 Chirality : 0.050 0.243 926 Planarity : 0.005 0.047 1090 Dihedral : 6.263 55.910 875 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.70 % Favored : 91.17 % Rotamer: Outliers : 7.17 % Allowed : 18.15 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -1.08 (0.31), residues: 770 helix: 0.58 (0.55), residues: 89 sheet: -0.34 (0.29), residues: 314 loop : -1.34 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 66 TYR 0.021 0.002 TYR A 59 PHE 0.014 0.003 PHE P 7 TRP 0.013 0.002 TRP B 95 HIS 0.010 0.002 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 6198) covalent geometry : angle 0.79561 ( 8452) SS BOND : bond 0.00928 ( 7) SS BOND : angle 1.88285 ( 14) hydrogen bonds : bond 0.05361 ( 233) hydrogen bonds : angle 7.30047 ( 693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 74 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: B 50 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5684 (tm-30) REVERT: B 51 MET cc_start: 0.7453 (ppp) cc_final: 0.6872 (ppp) REVERT: B 52 SER cc_start: 0.8427 (t) cc_final: 0.7074 (p) REVERT: B 53 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7448 (p0) REVERT: B 54 MET cc_start: 0.8121 (mpp) cc_final: 0.7608 (tpp) REVERT: L 47 MET cc_start: 0.7527 (mmm) cc_final: 0.7286 (mmm) REVERT: A 45 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: A 208 PHE cc_start: 0.5824 (p90) cc_final: 0.5398 (p90) REVERT: H 6 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: H 48 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8296 (tp30) REVERT: H 59 GLU cc_start: 0.8575 (mp0) cc_final: 0.8303 (mp0) REVERT: H 60 TYR cc_start: 0.7958 (m-80) cc_final: 0.7611 (m-80) REVERT: H 125 GLU cc_start: 0.9072 (tp30) cc_final: 0.8768 (tm-30) outliers start: 45 outliers final: 23 residues processed: 108 average time/residue: 0.4560 time to fit residues: 52.0169 Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 179 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 51 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.098984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.077841 restraints weight = 21020.018| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 4.83 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6205 Z= 0.181 Angle : 0.693 10.136 8466 Z= 0.349 Chirality : 0.046 0.191 926 Planarity : 0.004 0.048 1090 Dihedral : 5.992 58.458 875 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.66 % Favored : 92.21 % Rotamer: Outliers : 6.37 % Allowed : 20.70 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -1.13 (0.31), residues: 770 helix: 0.61 (0.55), residues: 89 sheet: -0.27 (0.30), residues: 295 loop : -1.45 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 81 TYR 0.017 0.002 TYR L 94 PHE 0.016 0.002 PHE H 176 TRP 0.010 0.002 TRP B 95 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 6198) covalent geometry : angle 0.69172 ( 8452) SS BOND : bond 0.00480 ( 7) SS BOND : angle 1.12402 ( 14) hydrogen bonds : bond 0.04209 ( 233) hydrogen bonds : angle 6.66394 ( 693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 84 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: B 51 MET cc_start: 0.7227 (ppp) cc_final: 0.6938 (ppp) REVERT: B 52 SER cc_start: 0.8206 (t) cc_final: 0.7190 (p) REVERT: B 53 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7386 (p0) REVERT: B 54 MET cc_start: 0.7756 (mpp) cc_final: 0.7328 (tpp) REVERT: B 96 ASP cc_start: 0.8259 (p0) cc_final: 0.8002 (p0) REVERT: B 97 ARG cc_start: 0.7483 (mmp80) cc_final: 0.6882 (mmp80) REVERT: A 45 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: A 70 ASN cc_start: 0.8434 (m-40) cc_final: 0.8112 (m-40) REVERT: A 186 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8491 (mmtm) REVERT: A 208 PHE cc_start: 0.5938 (p90) cc_final: 0.5532 (p90) REVERT: A 264 GLU cc_start: 0.2926 (OUTLIER) cc_final: 0.2579 (mp0) REVERT: H 60 TYR cc_start: 0.7783 (m-80) cc_final: 0.7383 (m-80) REVERT: H 155 TYR cc_start: 0.7773 (p90) cc_final: 0.7200 (p90) outliers start: 40 outliers final: 18 residues processed: 117 average time/residue: 0.4281 time to fit residues: 53.1154 Evaluate side-chains 97 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 176 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 7 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 53 optimal weight: 0.0370 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.100332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.080812 restraints weight = 21259.452| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 4.65 r_work: 0.3713 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6205 Z= 0.150 Angle : 0.708 10.446 8466 Z= 0.350 Chirality : 0.045 0.160 926 Planarity : 0.004 0.048 1090 Dihedral : 5.890 59.488 873 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.92 % Favored : 91.95 % Rotamer: Outliers : 6.21 % Allowed : 21.18 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -1.05 (0.31), residues: 770 helix: 0.71 (0.56), residues: 89 sheet: -0.32 (0.30), residues: 300 loop : -1.33 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 81 TYR 0.020 0.002 TYR L 192 PHE 0.022 0.001 PHE P 7 TRP 0.010 0.001 TRP A 204 HIS 0.004 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6198) covalent geometry : angle 0.70698 ( 8452) SS BOND : bond 0.00469 ( 7) SS BOND : angle 1.00399 ( 14) hydrogen bonds : bond 0.04005 ( 233) hydrogen bonds : angle 6.32957 ( 693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7400 (mp10) REVERT: B 51 MET cc_start: 0.7405 (ppp) cc_final: 0.7165 (ppp) REVERT: B 52 SER cc_start: 0.8313 (t) cc_final: 0.7389 (p) REVERT: B 53 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7464 (p0) REVERT: B 54 MET cc_start: 0.7831 (mpp) cc_final: 0.7598 (tpp) REVERT: A 45 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: A 70 ASN cc_start: 0.8542 (m-40) cc_final: 0.8229 (m-40) REVERT: A 98 MET cc_start: 0.8671 (ttt) cc_final: 0.7557 (ttt) REVERT: A 186 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8506 (mmtm) REVERT: A 208 PHE cc_start: 0.5853 (p90) cc_final: 0.5496 (p90) REVERT: A 264 GLU cc_start: 0.3177 (OUTLIER) cc_final: 0.2844 (mp0) REVERT: H 6 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: H 59 GLU cc_start: 0.8599 (mp0) cc_final: 0.8319 (mp0) REVERT: H 60 TYR cc_start: 0.7951 (m-80) cc_final: 0.7549 (m-80) REVERT: H 155 TYR cc_start: 0.7921 (p90) cc_final: 0.7323 (p90) outliers start: 39 outliers final: 19 residues processed: 112 average time/residue: 0.4484 time to fit residues: 52.9937 Evaluate side-chains 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 175 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 14 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN H 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.101795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.082346 restraints weight = 21083.984| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 4.67 r_work: 0.3737 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6205 Z= 0.131 Angle : 0.721 11.429 8466 Z= 0.352 Chirality : 0.045 0.170 926 Planarity : 0.004 0.052 1090 Dihedral : 5.796 59.657 873 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.40 % Favored : 92.47 % Rotamer: Outliers : 6.69 % Allowed : 21.18 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -1.00 (0.31), residues: 770 helix: 0.71 (0.56), residues: 89 sheet: -0.25 (0.30), residues: 291 loop : -1.29 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 81 TYR 0.018 0.001 TYR B 10 PHE 0.010 0.001 PHE A 116 TRP 0.013 0.001 TRP A 204 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6198) covalent geometry : angle 0.71831 ( 8452) SS BOND : bond 0.00405 ( 7) SS BOND : angle 1.72032 ( 14) hydrogen bonds : bond 0.03774 ( 233) hydrogen bonds : angle 6.06008 ( 693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 82 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.7257 (ppp) cc_final: 0.6969 (ppp) REVERT: B 52 SER cc_start: 0.8145 (t) cc_final: 0.7523 (p) REVERT: B 53 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7289 (p0) REVERT: B 54 MET cc_start: 0.7993 (mpp) cc_final: 0.7518 (tpp) REVERT: B 91 LYS cc_start: 0.8384 (mttt) cc_final: 0.8172 (mtpp) REVERT: A 70 ASN cc_start: 0.8536 (m-40) cc_final: 0.8218 (m-40) REVERT: A 208 PHE cc_start: 0.5854 (p90) cc_final: 0.5452 (p90) REVERT: A 264 GLU cc_start: 0.3183 (OUTLIER) cc_final: 0.2843 (mp0) REVERT: H 12 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8877 (mp) REVERT: H 59 GLU cc_start: 0.8456 (mp0) cc_final: 0.8239 (mp0) REVERT: H 60 TYR cc_start: 0.7923 (m-80) cc_final: 0.7519 (m-80) REVERT: H 88 ASP cc_start: 0.8755 (t0) cc_final: 0.8322 (t70) REVERT: H 155 TYR cc_start: 0.7829 (p90) cc_final: 0.7242 (p90) outliers start: 42 outliers final: 19 residues processed: 113 average time/residue: 0.4220 time to fit residues: 50.5609 Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 175 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.102145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.082891 restraints weight = 20843.200| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 4.58 r_work: 0.3757 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6205 Z= 0.134 Angle : 0.751 11.844 8466 Z= 0.364 Chirality : 0.046 0.228 926 Planarity : 0.004 0.049 1090 Dihedral : 5.752 59.620 872 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.53 % Favored : 92.34 % Rotamer: Outliers : 5.10 % Allowed : 22.77 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -0.87 (0.31), residues: 770 helix: 0.72 (0.56), residues: 89 sheet: -0.12 (0.31), residues: 293 loop : -1.24 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.018 0.001 TYR L 192 PHE 0.009 0.001 PHE A 116 TRP 0.014 0.001 TRP A 217 HIS 0.003 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6198) covalent geometry : angle 0.74879 ( 8452) SS BOND : bond 0.00439 ( 7) SS BOND : angle 1.46236 ( 14) hydrogen bonds : bond 0.03787 ( 233) hydrogen bonds : angle 6.01293 ( 693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.7217 (ppp) cc_final: 0.6840 (ppp) REVERT: B 52 SER cc_start: 0.8012 (t) cc_final: 0.7343 (p) REVERT: B 53 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7053 (p0) REVERT: B 54 MET cc_start: 0.7967 (mpp) cc_final: 0.7500 (tpp) REVERT: L 11 MET cc_start: 0.7335 (tpp) cc_final: 0.7125 (tpp) REVERT: L 94 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6714 (t80) REVERT: L 212 ASN cc_start: 0.9163 (p0) cc_final: 0.8799 (m110) REVERT: A 45 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: A 70 ASN cc_start: 0.8552 (m-40) cc_final: 0.8284 (m-40) REVERT: A 141 GLN cc_start: 0.8926 (mp10) cc_final: 0.8544 (mp10) REVERT: A 186 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8479 (mmpt) REVERT: A 264 GLU cc_start: 0.3196 (OUTLIER) cc_final: 0.2862 (mp0) REVERT: H 4 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6735 (tp) REVERT: H 12 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8865 (mp) REVERT: H 56 ASP cc_start: 0.8355 (m-30) cc_final: 0.7978 (m-30) REVERT: H 59 GLU cc_start: 0.8603 (mp0) cc_final: 0.8301 (mp0) REVERT: H 60 TYR cc_start: 0.7938 (m-80) cc_final: 0.7430 (m-80) REVERT: H 88 ASP cc_start: 0.8820 (t0) cc_final: 0.8391 (t70) REVERT: H 155 TYR cc_start: 0.7869 (p90) cc_final: 0.7315 (p90) outliers start: 32 outliers final: 19 residues processed: 104 average time/residue: 0.4191 time to fit residues: 46.1841 Evaluate side-chains 98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 175 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN L 31 ASN A 96 GLN ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.094765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.074175 restraints weight = 21487.130| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 5.15 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6205 Z= 0.282 Angle : 0.830 11.095 8466 Z= 0.416 Chirality : 0.048 0.201 926 Planarity : 0.005 0.048 1090 Dihedral : 6.178 57.198 871 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.96 % Favored : 90.91 % Rotamer: Outliers : 5.41 % Allowed : 22.93 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -1.33 (0.31), residues: 770 helix: 0.45 (0.55), residues: 89 sheet: -0.46 (0.29), residues: 301 loop : -1.54 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 202 TYR 0.058 0.002 TYR A 22 PHE 0.011 0.002 PHE H 156 TRP 0.012 0.002 TRP A 147 HIS 0.008 0.002 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00624 ( 6198) covalent geometry : angle 0.82538 ( 8452) SS BOND : bond 0.00639 ( 7) SS BOND : angle 2.30367 ( 14) hydrogen bonds : bond 0.04642 ( 233) hydrogen bonds : angle 6.54953 ( 693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 SER cc_start: 0.8072 (t) cc_final: 0.6896 (p) REVERT: B 54 MET cc_start: 0.7895 (mpp) cc_final: 0.7221 (tpp) REVERT: B 91 LYS cc_start: 0.8429 (mttt) cc_final: 0.7827 (mttt) REVERT: A 264 GLU cc_start: 0.2800 (OUTLIER) cc_final: 0.2585 (mp0) REVERT: H 6 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: H 12 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8919 (mp) REVERT: H 30 SER cc_start: 0.8772 (t) cc_final: 0.8492 (p) REVERT: H 56 ASP cc_start: 0.8244 (m-30) cc_final: 0.7838 (m-30) REVERT: H 60 TYR cc_start: 0.7825 (m-80) cc_final: 0.7316 (m-80) REVERT: H 88 ASP cc_start: 0.8677 (t0) cc_final: 0.8310 (t70) REVERT: H 155 TYR cc_start: 0.7895 (p90) cc_final: 0.7355 (p90) outliers start: 34 outliers final: 22 residues processed: 102 average time/residue: 0.4057 time to fit residues: 44.1183 Evaluate side-chains 89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 179 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 64 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 0.0770 chunk 72 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.100920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.081404 restraints weight = 21002.221| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 4.56 r_work: 0.3722 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6205 Z= 0.142 Angle : 0.788 12.477 8466 Z= 0.384 Chirality : 0.046 0.166 926 Planarity : 0.004 0.071 1090 Dihedral : 5.961 58.724 871 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.14 % Favored : 92.73 % Rotamer: Outliers : 4.14 % Allowed : 24.68 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -1.12 (0.31), residues: 770 helix: 0.38 (0.57), residues: 89 sheet: -0.33 (0.31), residues: 293 loop : -1.32 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 145 TYR 0.041 0.002 TYR A 22 PHE 0.011 0.001 PHE A 116 TRP 0.022 0.002 TRP L 148 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6198) covalent geometry : angle 0.78748 ( 8452) SS BOND : bond 0.00610 ( 7) SS BOND : angle 1.24307 ( 14) hydrogen bonds : bond 0.03867 ( 233) hydrogen bonds : angle 5.97817 ( 693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.7237 (ppp) cc_final: 0.6826 (ppp) REVERT: B 52 SER cc_start: 0.7937 (t) cc_final: 0.7298 (p) REVERT: B 54 MET cc_start: 0.8106 (mpp) cc_final: 0.7393 (tpp) REVERT: L 42 LYS cc_start: 0.8217 (mmmm) cc_final: 0.7985 (mmmm) REVERT: L 47 MET cc_start: 0.7025 (mmm) cc_final: 0.6713 (mpm) REVERT: L 94 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.6690 (t80) REVERT: A 45 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: A 70 ASN cc_start: 0.8722 (m-40) cc_final: 0.8438 (m-40) REVERT: A 141 GLN cc_start: 0.8872 (mp10) cc_final: 0.8482 (mp10) REVERT: A 264 GLU cc_start: 0.3109 (OUTLIER) cc_final: 0.2847 (mp0) REVERT: H 12 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8860 (mp) REVERT: H 30 SER cc_start: 0.8874 (t) cc_final: 0.8619 (p) REVERT: H 56 ASP cc_start: 0.8245 (m-30) cc_final: 0.7850 (m-30) REVERT: H 60 TYR cc_start: 0.7966 (m-80) cc_final: 0.7460 (m-80) REVERT: H 88 ASP cc_start: 0.8737 (t0) cc_final: 0.8328 (t70) REVERT: H 155 TYR cc_start: 0.7958 (p90) cc_final: 0.7374 (p90) outliers start: 26 outliers final: 21 residues processed: 103 average time/residue: 0.4132 time to fit residues: 45.2366 Evaluate side-chains 97 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.098433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.079229 restraints weight = 20935.920| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 4.97 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6205 Z= 0.207 Angle : 0.821 12.864 8466 Z= 0.404 Chirality : 0.046 0.181 926 Planarity : 0.005 0.069 1090 Dihedral : 6.103 58.206 871 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.22 % Favored : 90.65 % Rotamer: Outliers : 4.30 % Allowed : 25.48 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -1.21 (0.31), residues: 770 helix: 0.36 (0.57), residues: 89 sheet: -0.39 (0.30), residues: 303 loop : -1.40 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.040 0.002 TYR A 22 PHE 0.033 0.002 PHE P 7 TRP 0.038 0.002 TRP H 49 HIS 0.005 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 6198) covalent geometry : angle 0.81864 ( 8452) SS BOND : bond 0.00545 ( 7) SS BOND : angle 1.84937 ( 14) hydrogen bonds : bond 0.04139 ( 233) hydrogen bonds : angle 6.19654 ( 693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.7198 (ppp) cc_final: 0.6768 (ppp) REVERT: B 52 SER cc_start: 0.8033 (t) cc_final: 0.7305 (p) REVERT: B 54 MET cc_start: 0.7933 (mpp) cc_final: 0.7332 (tpp) REVERT: B 87 MET cc_start: 0.7767 (mtp) cc_final: 0.7259 (ttp) REVERT: B 91 LYS cc_start: 0.8336 (mttt) cc_final: 0.8026 (mttt) REVERT: L 42 LYS cc_start: 0.8400 (mmmm) cc_final: 0.8156 (mmmm) REVERT: L 161 ASP cc_start: 0.8496 (p0) cc_final: 0.8286 (p0) REVERT: A 45 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: A 141 GLN cc_start: 0.8824 (mp10) cc_final: 0.8412 (mp10) REVERT: A 264 GLU cc_start: 0.2974 (OUTLIER) cc_final: 0.2760 (mp0) REVERT: H 6 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6592 (mt-10) REVERT: H 12 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8865 (mp) REVERT: H 30 SER cc_start: 0.8768 (t) cc_final: 0.8478 (p) REVERT: H 56 ASP cc_start: 0.8148 (m-30) cc_final: 0.7735 (m-30) REVERT: H 60 TYR cc_start: 0.7915 (m-80) cc_final: 0.7287 (m-80) REVERT: H 88 ASP cc_start: 0.8626 (t0) cc_final: 0.8287 (t70) REVERT: H 155 TYR cc_start: 0.7839 (p90) cc_final: 0.7311 (p90) outliers start: 27 outliers final: 19 residues processed: 95 average time/residue: 0.4007 time to fit residues: 40.5374 Evaluate side-chains 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 40.0000 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.099514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.080115 restraints weight = 20819.401| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 4.53 r_work: 0.3708 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6205 Z= 0.163 Angle : 0.795 12.317 8466 Z= 0.387 Chirality : 0.046 0.166 926 Planarity : 0.004 0.064 1090 Dihedral : 6.059 58.797 871 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.44 % Favored : 91.43 % Rotamer: Outliers : 3.66 % Allowed : 25.48 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -1.15 (0.31), residues: 770 helix: 0.39 (0.57), residues: 89 sheet: -0.33 (0.30), residues: 303 loop : -1.38 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.040 0.002 TYR A 22 PHE 0.028 0.002 PHE H 156 TRP 0.033 0.002 TRP H 49 HIS 0.003 0.001 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6198) covalent geometry : angle 0.79359 ( 8452) SS BOND : bond 0.00420 ( 7) SS BOND : angle 1.51138 ( 14) hydrogen bonds : bond 0.03874 ( 233) hydrogen bonds : angle 5.99382 ( 693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.53 seconds wall clock time: 41 minutes 12.27 seconds (2472.27 seconds total)