Starting phenix.real_space_refine on Wed Mar 4 12:43:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk3_25171/03_2026/7sk3_25171_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk3_25171/03_2026/7sk3_25171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sk3_25171/03_2026/7sk3_25171_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk3_25171/03_2026/7sk3_25171_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sk3_25171/03_2026/7sk3_25171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk3_25171/03_2026/7sk3_25171.map" } resolution = 3.8 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= -0.002 sd= 0.073 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 4480 2.51 5 N 1079 2.21 5 O 1206 1.98 5 H 6491 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 13294 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4967 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 11, 'TRANS': 292} Chain: "B" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1145 Classifications: {'peptide': 68} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "C" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1592 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1888 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "E" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1607 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "F" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1871 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 224 Unusual residues: {'CLR': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 2.43, per 1000 atoms: 0.18 Number of scatterers: 13294 At special positions: 0 Unit cell: (70.2, 71.28, 146.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 O 1206 8.00 N 1079 7.00 C 4480 6.00 H 6491 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " 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: 0.96 Conformation dependent library (CDL) restraints added in 396.5 milliseconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 15 sheets defined 34.5% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 40 through 73 removed outlier: 3.824A pdb=" N ALA A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.579A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.642A pdb=" N TRP A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 148 removed outlier: 3.939A pdb=" N SER A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 153 through 182 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 204 through 219 removed outlier: 4.272A pdb=" N SER A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 242 Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.590A pdb=" N LYS A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 280 removed outlier: 4.362A pdb=" N ILE A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.575A pdb=" N LEU A 273 " --> pdb=" O HIS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 311 removed outlier: 3.878A pdb=" N GLU A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS A 291 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.751A pdb=" N VAL B 23 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 65 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 3.583A pdb=" N VAL A 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 30 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.705A pdb=" N SER F 112 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 187 Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.119A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AA8, first strand: chain 'D' and resid 6 through 10 Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.574A pdb=" N SER D 62 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR D 117 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.574A pdb=" N SER D 62 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.691A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.638A pdb=" N GLN E 91 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AB6, first strand: chain 'F' and resid 61 through 63 removed outlier: 3.694A pdb=" N SER F 62 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER F 53 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER F 36 " --> pdb=" O VAL F 102 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6480 1.03 - 1.23: 18 1.23 - 1.42: 2983 1.42 - 1.62: 3967 1.62 - 1.81: 51 Bond restraints: 13499 Sorted by residual: bond pdb=" C6 CLR A 608 " pdb=" C7 CLR A 608 " ideal model delta sigma weight residual 1.492 1.541 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C6 CLR A 607 " pdb=" C7 CLR A 607 " ideal model delta sigma weight residual 1.492 1.541 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C6 CLR A 605 " pdb=" C7 CLR A 605 " ideal model delta sigma weight residual 1.492 1.538 -0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C6 CLR A 604 " pdb=" C7 CLR A 604 " ideal model delta sigma weight residual 1.492 1.538 -0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" C6 CLR A 606 " pdb=" C7 CLR A 606 " ideal model delta sigma weight residual 1.492 1.538 -0.046 2.00e-02 2.50e+03 5.29e+00 ... (remaining 13494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 23859 1.69 - 3.38: 269 3.38 - 5.07: 50 5.07 - 6.76: 22 6.76 - 8.45: 8 Bond angle restraints: 24208 Sorted by residual: angle pdb=" C22 CLR A 602 " pdb=" C23 CLR A 602 " pdb=" C24 CLR A 602 " ideal model delta sigma weight residual 111.95 103.50 8.45 3.00e+00 1.11e-01 7.93e+00 angle pdb=" C22 CLR A 605 " pdb=" C23 CLR A 605 " pdb=" C24 CLR A 605 " ideal model delta sigma weight residual 111.95 103.66 8.29 3.00e+00 1.11e-01 7.64e+00 angle pdb=" C22 CLR A 604 " pdb=" C23 CLR A 604 " pdb=" C24 CLR A 604 " ideal model delta sigma weight residual 111.95 103.81 8.14 3.00e+00 1.11e-01 7.36e+00 angle pdb=" C22 CLR A 603 " pdb=" C23 CLR A 603 " pdb=" C24 CLR A 603 " ideal model delta sigma weight residual 111.95 103.94 8.01 3.00e+00 1.11e-01 7.13e+00 angle pdb=" C22 CLR A 608 " pdb=" C23 CLR A 608 " pdb=" C24 CLR A 608 " ideal model delta sigma weight residual 111.95 104.02 7.93 3.00e+00 1.11e-01 7.00e+00 ... (remaining 24203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6249 17.78 - 35.56: 484 35.56 - 53.34: 112 53.34 - 71.12: 19 71.12 - 88.90: 5 Dihedral angle restraints: 6869 sinusoidal: 3824 harmonic: 3045 Sorted by residual: dihedral pdb=" CA TYR D 55 " pdb=" C TYR D 55 " pdb=" N SER D 56 " pdb=" CA SER D 56 " ideal model delta harmonic sigma weight residual -180.00 -159.89 -20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA HIS A 269 " pdb=" C HIS A 269 " pdb=" N VAL A 270 " pdb=" CA VAL A 270 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLY C 69 " pdb=" C GLY C 69 " pdb=" N THR C 70 " pdb=" CA THR C 70 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 979 0.080 - 0.161: 86 0.161 - 0.241: 2 0.241 - 0.321: 22 0.321 - 0.402: 8 Chirality restraints: 1097 Sorted by residual: chirality pdb=" C17 CLR A 606 " pdb=" C13 CLR A 606 " pdb=" C16 CLR A 606 " pdb=" C20 CLR A 606 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C17 CLR A 608 " pdb=" C13 CLR A 608 " pdb=" C16 CLR A 608 " pdb=" C20 CLR A 608 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C17 CLR A 604 " pdb=" C13 CLR A 604 " pdb=" C16 CLR A 604 " pdb=" C20 CLR A 604 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 1094 not shown) Planarity restraints: 1921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 80 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO E 81 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 12 " -0.111 9.50e-02 1.11e+02 3.70e-02 1.59e+00 pdb=" NE ARG B 12 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 12 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 12 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 12 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG B 12 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 12 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 12 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 12 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 40 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO C 41 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.015 5.00e-02 4.00e+02 ... (remaining 1918 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2238 2.28 - 2.86: 28788 2.86 - 3.44: 31611 3.44 - 4.02: 45014 4.02 - 4.60: 67718 Nonbonded interactions: 175369 Sorted by model distance: nonbonded pdb=" OE2 GLU F 9 " pdb=" H CYS F 99 " model vdw 1.697 2.450 nonbonded pdb=" HH TYR C 37 " pdb=" OE1 GLN C 90 " model vdw 1.727 2.450 nonbonded pdb=" HE ARG F 41 " pdb=" OE2 GLU F 49 " model vdw 1.762 2.450 nonbonded pdb=" OE1 GLU C 82 " pdb=" H GLU C 82 " model vdw 1.779 2.450 nonbonded pdb="HE22 GLN A 245 " pdb=" O TYR F 104 " model vdw 1.786 2.450 ... (remaining 175364 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 3 through 91 or resid 93 through 94 or resid 98 through 10 \ 7)) selection = (chain 'E' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 4 through 54 or (resid 55 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB \ 3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or \ name HD23)) or resid 56 through 91 or resid 93 through 94 or resid 98 through 1 \ 07)) } ncs_group { reference = (chain 'D' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 6 through 31 or resid 33 o \ r resid 35 through 52 or resid 54 or resid 57 through 102 or resid 105 through 1 \ 06 or resid 111 or resid 113 or resid 116 through 127)) selection = (chain 'F' and (resid 5 through 31 or resid 33 or resid 35 through 52 or resid 5 \ 4 or resid 57 through 102 or resid 105 or resid 109 or resid 114 or resid 116 or \ resid 118 through 129)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.070 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.090 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 0.049 7015 Z= 0.231 Angle : 0.677 8.449 9606 Z= 0.281 Chirality : 0.067 0.402 1097 Planarity : 0.003 0.049 1131 Dihedral : 13.105 88.900 2881 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.31), residues: 819 helix: 1.65 (0.35), residues: 239 sheet: 0.12 (0.38), residues: 216 loop : -0.94 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 12 TYR 0.009 0.001 TYR D 55 PHE 0.008 0.001 PHE A 53 TRP 0.009 0.001 TRP C 36 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 7008) covalent geometry : angle 0.67681 ( 9592) SS BOND : bond 0.00241 ( 7) SS BOND : angle 0.83547 ( 14) hydrogen bonds : bond 0.18188 ( 318) hydrogen bonds : angle 6.57519 ( 921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8507 (t80) cc_final: 0.8295 (t80) REVERT: A 79 THR cc_start: 0.8984 (p) cc_final: 0.8759 (p) REVERT: C 107 ILE cc_start: 0.7209 (mp) cc_final: 0.6672 (mp) REVERT: F 93 ASP cc_start: 0.8440 (t0) cc_final: 0.8014 (t0) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1842 time to fit residues: 33.6029 Evaluate side-chains 117 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0030 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.092884 restraints weight = 28867.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.096658 restraints weight = 16268.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099131 restraints weight = 10754.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.100803 restraints weight = 7851.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.101892 restraints weight = 6166.886| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7015 Z= 0.133 Angle : 0.499 4.862 9606 Z= 0.270 Chirality : 0.040 0.138 1097 Planarity : 0.003 0.039 1131 Dihedral : 5.577 59.101 1438 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.96 % Allowed : 6.31 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.31), residues: 819 helix: 1.67 (0.34), residues: 242 sheet: 0.14 (0.37), residues: 217 loop : -1.05 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.010 0.001 TYR D 117 PHE 0.008 0.001 PHE A 231 TRP 0.006 0.001 TRP D 50 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7008) covalent geometry : angle 0.49818 ( 9592) SS BOND : bond 0.00349 ( 7) SS BOND : angle 0.89312 ( 14) hydrogen bonds : bond 0.05846 ( 318) hydrogen bonds : angle 5.26694 ( 921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.7809 (m-30) cc_final: 0.7592 (m-30) REVERT: F 93 ASP cc_start: 0.8407 (t0) cc_final: 0.8181 (t0) outliers start: 7 outliers final: 6 residues processed: 127 average time/residue: 0.1803 time to fit residues: 30.7868 Evaluate side-chains 122 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.091457 restraints weight = 29476.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.095016 restraints weight = 16938.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.097417 restraints weight = 11344.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.098920 restraints weight = 8363.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.100062 restraints weight = 6684.107| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7015 Z= 0.165 Angle : 0.503 5.960 9606 Z= 0.271 Chirality : 0.040 0.134 1097 Planarity : 0.003 0.041 1131 Dihedral : 5.273 55.285 1438 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.65 % Allowed : 7.41 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.30), residues: 819 helix: 1.64 (0.34), residues: 242 sheet: 0.10 (0.37), residues: 219 loop : -1.08 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.011 0.001 TYR D 117 PHE 0.009 0.001 PHE A 149 TRP 0.007 0.001 TRP D 50 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7008) covalent geometry : angle 0.50244 ( 9592) SS BOND : bond 0.00366 ( 7) SS BOND : angle 0.85077 ( 14) hydrogen bonds : bond 0.05450 ( 318) hydrogen bonds : angle 5.02948 ( 921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8333 (t80) cc_final: 0.8089 (t80) REVERT: D 116 ASP cc_start: 0.7595 (m-30) cc_final: 0.7354 (m-30) REVERT: F 93 ASP cc_start: 0.8390 (t0) cc_final: 0.8124 (t0) outliers start: 12 outliers final: 12 residues processed: 121 average time/residue: 0.1689 time to fit residues: 27.4707 Evaluate side-chains 119 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.090870 restraints weight = 29349.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.094791 restraints weight = 16245.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.097280 restraints weight = 10619.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.099018 restraints weight = 7738.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.100164 restraints weight = 6077.334| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7015 Z= 0.153 Angle : 0.492 6.037 9606 Z= 0.264 Chirality : 0.040 0.134 1097 Planarity : 0.003 0.041 1131 Dihedral : 5.044 49.965 1438 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.06 % Allowed : 8.50 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.09 (0.30), residues: 819 helix: 1.69 (0.34), residues: 243 sheet: 0.21 (0.37), residues: 215 loop : -1.18 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.010 0.001 TYR D 117 PHE 0.009 0.001 PHE A 149 TRP 0.008 0.001 TRP D 50 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7008) covalent geometry : angle 0.49128 ( 9592) SS BOND : bond 0.00345 ( 7) SS BOND : angle 0.77444 ( 14) hydrogen bonds : bond 0.05063 ( 318) hydrogen bonds : angle 4.86364 ( 921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8281 (t80) cc_final: 0.8068 (t80) REVERT: D 116 ASP cc_start: 0.7649 (m-30) cc_final: 0.7448 (m-30) REVERT: F 93 ASP cc_start: 0.8410 (t0) cc_final: 0.8140 (t0) outliers start: 15 outliers final: 13 residues processed: 126 average time/residue: 0.1662 time to fit residues: 28.3294 Evaluate side-chains 125 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN E 4 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.091378 restraints weight = 29318.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.095193 restraints weight = 16163.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.097754 restraints weight = 10592.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.099374 restraints weight = 7685.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.100566 restraints weight = 6045.853| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7015 Z= 0.159 Angle : 0.498 6.259 9606 Z= 0.266 Chirality : 0.040 0.133 1097 Planarity : 0.003 0.041 1131 Dihedral : 5.054 46.344 1438 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.92 % Allowed : 10.97 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.05 (0.30), residues: 819 helix: 1.70 (0.34), residues: 243 sheet: 0.13 (0.37), residues: 215 loop : -1.19 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 25 TYR 0.010 0.001 TYR D 117 PHE 0.009 0.001 PHE A 149 TRP 0.007 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7008) covalent geometry : angle 0.49745 ( 9592) SS BOND : bond 0.00358 ( 7) SS BOND : angle 0.75209 ( 14) hydrogen bonds : bond 0.04963 ( 318) hydrogen bonds : angle 4.77540 ( 921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8461 (t80) cc_final: 0.8230 (t80) REVERT: B 15 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7183 (tm-30) REVERT: D 116 ASP cc_start: 0.7633 (m-30) cc_final: 0.7417 (m-30) REVERT: F 93 ASP cc_start: 0.8436 (t0) cc_final: 0.8148 (t0) outliers start: 14 outliers final: 14 residues processed: 124 average time/residue: 0.1692 time to fit residues: 28.1453 Evaluate side-chains 126 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.092194 restraints weight = 29179.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.095688 restraints weight = 16756.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.097906 restraints weight = 11232.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.099565 restraints weight = 8380.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.100564 restraints weight = 6618.376| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7015 Z= 0.160 Angle : 0.495 6.573 9606 Z= 0.265 Chirality : 0.040 0.133 1097 Planarity : 0.003 0.040 1131 Dihedral : 5.061 42.337 1438 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.33 % Allowed : 10.70 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.01 (0.30), residues: 819 helix: 1.72 (0.34), residues: 243 sheet: 0.04 (0.37), residues: 217 loop : -1.23 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 70 TYR 0.009 0.001 TYR D 53 PHE 0.010 0.001 PHE A 149 TRP 0.007 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7008) covalent geometry : angle 0.49454 ( 9592) SS BOND : bond 0.00370 ( 7) SS BOND : angle 0.76009 ( 14) hydrogen bonds : bond 0.04883 ( 318) hydrogen bonds : angle 4.70715 ( 921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7186 (tm-30) REVERT: D 116 ASP cc_start: 0.7666 (m-30) cc_final: 0.7452 (m-30) REVERT: F 93 ASP cc_start: 0.8427 (t0) cc_final: 0.8118 (t0) outliers start: 17 outliers final: 16 residues processed: 127 average time/residue: 0.1530 time to fit residues: 26.7406 Evaluate side-chains 131 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 0.0070 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN E 4 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.093295 restraints weight = 28942.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.096871 restraints weight = 16671.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.099268 restraints weight = 11188.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.100812 restraints weight = 8272.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.101903 restraints weight = 6579.977| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 0.042 7015 Z= 0.115 Angle : 0.466 6.581 9606 Z= 0.248 Chirality : 0.039 0.130 1097 Planarity : 0.003 0.039 1131 Dihedral : 4.806 38.670 1438 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.19 % Allowed : 10.97 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.18 (0.30), residues: 819 helix: 1.87 (0.34), residues: 243 sheet: 0.13 (0.37), residues: 217 loop : -1.11 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 12 TYR 0.008 0.001 TYR A 257 PHE 0.009 0.001 PHE A 149 TRP 0.007 0.001 TRP C 36 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7008) covalent geometry : angle 0.46604 ( 9592) SS BOND : bond 0.00344 ( 7) SS BOND : angle 0.61723 ( 14) hydrogen bonds : bond 0.04465 ( 318) hydrogen bonds : angle 4.54941 ( 921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7105 (tm-30) REVERT: D 116 ASP cc_start: 0.7602 (m-30) cc_final: 0.7393 (m-30) REVERT: F 93 ASP cc_start: 0.8362 (t0) cc_final: 0.8042 (t0) outliers start: 16 outliers final: 16 residues processed: 126 average time/residue: 0.1678 time to fit residues: 28.6865 Evaluate side-chains 126 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN E 101 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.091343 restraints weight = 29252.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.094918 restraints weight = 16938.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.097223 restraints weight = 11418.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.098868 restraints weight = 8501.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.099832 restraints weight = 6768.948| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7015 Z= 0.154 Angle : 0.494 6.575 9606 Z= 0.264 Chirality : 0.040 0.132 1097 Planarity : 0.003 0.038 1131 Dihedral : 4.945 37.609 1438 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.19 % Allowed : 11.93 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.30), residues: 819 helix: 1.87 (0.34), residues: 243 sheet: 0.10 (0.37), residues: 217 loop : -1.20 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 25 TYR 0.009 0.001 TYR D 53 PHE 0.016 0.001 PHE A 53 TRP 0.008 0.001 TRP C 36 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7008) covalent geometry : angle 0.49366 ( 9592) SS BOND : bond 0.00351 ( 7) SS BOND : angle 0.73033 ( 14) hydrogen bonds : bond 0.04704 ( 318) hydrogen bonds : angle 4.58173 ( 921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7187 (tm-30) REVERT: D 116 ASP cc_start: 0.7632 (m-30) cc_final: 0.7424 (m-30) REVERT: F 93 ASP cc_start: 0.8345 (t0) cc_final: 0.8031 (t0) outliers start: 16 outliers final: 16 residues processed: 122 average time/residue: 0.1631 time to fit residues: 27.0893 Evaluate side-chains 126 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN E 101 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.092039 restraints weight = 29345.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.095727 restraints weight = 16675.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.098201 restraints weight = 11089.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.099701 restraints weight = 8170.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.100871 restraints weight = 6552.921| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7015 Z= 0.137 Angle : 0.491 6.088 9606 Z= 0.261 Chirality : 0.040 0.130 1097 Planarity : 0.003 0.038 1131 Dihedral : 4.915 35.797 1438 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.33 % Allowed : 12.35 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.30), residues: 819 helix: 1.90 (0.34), residues: 243 sheet: 0.10 (0.37), residues: 217 loop : -1.18 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 12 TYR 0.008 0.001 TYR A 257 PHE 0.025 0.001 PHE A 49 TRP 0.010 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7008) covalent geometry : angle 0.49064 ( 9592) SS BOND : bond 0.00341 ( 7) SS BOND : angle 0.68169 ( 14) hydrogen bonds : bond 0.04558 ( 318) hydrogen bonds : angle 4.54650 ( 921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7130 (tm-30) REVERT: D 116 ASP cc_start: 0.7696 (m-30) cc_final: 0.7466 (m-30) REVERT: F 93 ASP cc_start: 0.8392 (t0) cc_final: 0.8062 (t0) outliers start: 17 outliers final: 17 residues processed: 119 average time/residue: 0.1614 time to fit residues: 26.0904 Evaluate side-chains 126 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN E 101 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.109311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.092649 restraints weight = 29261.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.096198 restraints weight = 16858.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.098574 restraints weight = 11304.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.100153 restraints weight = 8375.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.101152 restraints weight = 6654.985| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7015 Z= 0.152 Angle : 0.507 7.859 9606 Z= 0.269 Chirality : 0.040 0.130 1097 Planarity : 0.003 0.038 1131 Dihedral : 4.988 35.629 1438 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.33 % Allowed : 11.93 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.30), residues: 819 helix: 1.89 (0.34), residues: 243 sheet: 0.15 (0.37), residues: 215 loop : -1.24 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 12 TYR 0.009 0.001 TYR D 53 PHE 0.025 0.001 PHE A 49 TRP 0.011 0.001 TRP C 36 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7008) covalent geometry : angle 0.50675 ( 9592) SS BOND : bond 0.00342 ( 7) SS BOND : angle 0.71713 ( 14) hydrogen bonds : bond 0.04628 ( 318) hydrogen bonds : angle 4.54761 ( 921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7156 (tm-30) REVERT: C 106 GLU cc_start: 0.7901 (tp30) cc_final: 0.7633 (tp30) REVERT: D 116 ASP cc_start: 0.7664 (m-30) cc_final: 0.7440 (m-30) REVERT: F 93 ASP cc_start: 0.8400 (t0) cc_final: 0.8080 (t0) outliers start: 17 outliers final: 17 residues processed: 120 average time/residue: 0.1714 time to fit residues: 27.9222 Evaluate side-chains 127 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 15 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN E 101 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.094382 restraints weight = 28914.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.098139 restraints weight = 16344.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.100562 restraints weight = 10814.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.102038 restraints weight = 7956.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103209 restraints weight = 6365.683| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7015 Z= 0.122 Angle : 0.487 7.194 9606 Z= 0.257 Chirality : 0.039 0.129 1097 Planarity : 0.003 0.038 1131 Dihedral : 4.862 36.940 1438 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.33 % Allowed : 12.21 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.22 (0.31), residues: 819 helix: 1.96 (0.34), residues: 243 sheet: 0.18 (0.37), residues: 215 loop : -1.17 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 25 TYR 0.008 0.001 TYR C 37 PHE 0.025 0.001 PHE A 49 TRP 0.010 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7008) covalent geometry : angle 0.48708 ( 9592) SS BOND : bond 0.00327 ( 7) SS BOND : angle 0.62553 ( 14) hydrogen bonds : bond 0.04392 ( 318) hydrogen bonds : angle 4.47869 ( 921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.42 seconds wall clock time: 38 minutes 44.70 seconds (2324.70 seconds total)